From 0b2e939d4d739948c2a04ae056b50acc4d9bccf1 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 22 Aug 2012 16:12:59 -0400
Subject: [PATCH] Remove blast tools and test data from the distribution,
 update tool_conf.xml.sample to reflect this.

---
 .../test/tblastn_four_human_vs_rhodopsin.xml  | 722 ------------------
 test-data/tblastn_four_human_vs_rhodopsin.xml | 722 ------------------
 tool_conf.xml.sample                          |   8 -
 tools/ncbi_blast_plus/blastxml_to_tabular.py  | 254 ------
 tools/ncbi_blast_plus/blastxml_to_tabular.xml | 127 ---
 tools/ncbi_blast_plus/hide_stderr.py          |  49 --
 tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml | 211 -----
 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml | 278 -------
 tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml | 242 ------
 .../ncbi_blast_plus/ncbi_tblastn_wrapper.xml  | 288 -------
 .../ncbi_blast_plus/ncbi_tblastx_wrapper.xml  | 208 -----
 11 files changed, 3109 deletions(-)
 delete mode 100644 lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml
 delete mode 100644 test-data/tblastn_four_human_vs_rhodopsin.xml
 delete mode 100644 tools/ncbi_blast_plus/blastxml_to_tabular.py
 delete mode 100644 tools/ncbi_blast_plus/blastxml_to_tabular.xml
 delete mode 100755 tools/ncbi_blast_plus/hide_stderr.py
 delete mode 100644 tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
 delete mode 100644 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
 delete mode 100644 tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
 delete mode 100644 tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
 delete mode 100644 tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml

diff --git a/lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml b/lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml
deleted file mode 100644
index 9bccf112f2d..00000000000
--- a/lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml
+++ /dev/null
@@ -1,722 +0,0 @@
-<?xml version="1.0"?>
-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
-<BlastOutput>
-  <BlastOutput_program>tblastn</BlastOutput_program>
-  <BlastOutput_version>TBLASTN 2.2.25+</BlastOutput_version>
-  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
-  <BlastOutput_db></BlastOutput_db>
-  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
-  <BlastOutput_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</BlastOutput_query-def>
-  <BlastOutput_query-len>406</BlastOutput_query-len>
-  <BlastOutput_param>
-    <Parameters>
-      <Parameters_matrix>BLOSUM80</Parameters_matrix>
-      <Parameters_expect>1e-10</Parameters_expect>
-      <Parameters_gap-open>10</Parameters_gap-open>
-      <Parameters_gap-extend>1</Parameters_gap-extend>
-      <Parameters_filter>F</Parameters_filter>
-    </Parameters>
-  </BlastOutput_param>
-  <BlastOutput_iterations>
-    <Iteration>
-      <Iteration_iter-num>1</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>2</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>3</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>4</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>5</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>6</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>7</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>8</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>9</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>10</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>11</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>12</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>13</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>14</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>15</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>16</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>17</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>18</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>19</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_1</Hit_id>
-          <Hit_def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Hit_def>
-          <Hit_accession>Subject_1</Hit_accession>
-          <Hit_len>1047</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>732.392902459534</Hsp_bit-score>
-              <Hsp_score>1689</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>348</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>1044</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>1</Hsp_hit-frame>
-              <Hsp_identity>336</Hsp_identity>
-              <Hsp_positive>343</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>348</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>20</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_2</Hit_id>
-          <Hit_def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Hit_def>
-          <Hit_accession>Subject_2</Hit_accession>
-          <Hit_len>1574</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>646.119739014374</Hsp_bit-score>
-              <Hsp_score>1489</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>341</Hsp_query-to>
-              <Hsp_hit-from>42</Hsp_hit-from>
-              <Hsp_hit-to>1067</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>3</Hsp_hit-frame>
-              <Hsp_identity>290</Hsp_identity>
-              <Hsp_positive>320</Hsp_positive>
-              <Hsp_gaps>1</Hsp_gaps>
-              <Hsp_align-len>342</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S+ GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF+ QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA  SKTE</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>21</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_3</Hit_id>
-          <Hit_def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Hit_def>
-          <Hit_accession>Subject_3</Hit_accession>
-          <Hit_len>4301</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>151.343146656381</Hsp_bit-score>
-              <Hsp_score>342</Hsp_score>
-              <Hsp_evalue>1.39566684546685e-72</Hsp_evalue>
-              <Hsp_query-from>239</Hsp_query-from>
-              <Hsp_query-to>312</Hsp_query-to>
-              <Hsp_hit-from>3147</Hsp_hit-from>
-              <Hsp_hit-to>3368</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>3</Hsp_hit-frame>
-              <Hsp_identity>69</Hsp_identity>
-              <Hsp_positive>73</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>74</Hsp_align-len>
-              <Hsp_qseq>ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ</Hsp_qseq>
-              <Hsp_hseq>ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ</Hsp_hseq>
-              <Hsp_midline>ESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQ</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>2</Hsp_num>
-              <Hsp_bit-score>126.323929257285</Hsp_bit-score>
-              <Hsp_score>284</Hsp_score>
-              <Hsp_evalue>1.39566684546685e-72</Hsp_evalue>
-              <Hsp_query-from>177</Hsp_query-from>
-              <Hsp_query-to>235</Hsp_query-to>
-              <Hsp_hit-from>2855</Hsp_hit-from>
-              <Hsp_hit-to>3031</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>2</Hsp_hit-frame>
-              <Hsp_identity>54</Hsp_identity>
-              <Hsp_positive>57</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>59</Hsp_align-len>
-              <Hsp_qseq>RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA</Hsp_qseq>
-              <Hsp_hseq>RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS</Hsp_hseq>
-              <Hsp_midline>RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE  +</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>3</Hsp_num>
-              <Hsp_bit-score>229.420359574251</Hsp_bit-score>
-              <Hsp_score>523</Hsp_score>
-              <Hsp_evalue>9.84654801241353e-65</Hsp_evalue>
-              <Hsp_query-from>11</Hsp_query-from>
-              <Hsp_query-to>121</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>333</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>1</Hsp_hit-frame>
-              <Hsp_identity>107</Hsp_identity>
-              <Hsp_positive>109</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>111</Hsp_align-len>
-              <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_qseq>
-              <Hsp_hseq>VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_hseq>
-              <Hsp_midline>VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>4</Hsp_num>
-              <Hsp_bit-score>122.873002719478</Hsp_bit-score>
-              <Hsp_score>276</Hsp_score>
-              <Hsp_evalue>1.40732096096596e-32</Hsp_evalue>
-              <Hsp_query-from>119</Hsp_query-from>
-              <Hsp_query-to>177</Hsp_query-to>
-              <Hsp_hit-from>1404</Hsp_hit-from>
-              <Hsp_hit-to>1580</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>3</Hsp_hit-frame>
-              <Hsp_identity>55</Hsp_identity>
-              <Hsp_positive>56</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>59</Hsp_align-len>
-              <Hsp_qseq>LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR</Hsp_qseq>
-              <Hsp_hseq>LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR</Hsp_hseq>
-              <Hsp_midline>L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>5</Hsp_num>
-              <Hsp_bit-score>57.7367643183824</Hsp_bit-score>
-              <Hsp_score>125</Hsp_score>
-              <Hsp_evalue>5.60065526485586e-13</Hsp_evalue>
-              <Hsp_query-from>312</Hsp_query-from>
-              <Hsp_query-to>337</Hsp_query-to>
-              <Hsp_hit-from>4222</Hsp_hit-from>
-              <Hsp_hit-to>4299</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>1</Hsp_hit-frame>
-              <Hsp_identity>23</Hsp_identity>
-              <Hsp_positive>24</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>26</Hsp_align-len>
-              <Hsp_qseq>QFRNCMLTTICCGKNPLGDDEASATV</Hsp_qseq>
-              <Hsp_hseq>QFRNCMLTTLCCGKNPLGDDEASTTA</Hsp_hseq>
-              <Hsp_midline>QFRNCMLTT+CCGKNPLGDDEAS T </Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>22</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_4</Hit_id>
-          <Hit_def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Hit_def>
-          <Hit_accession>Subject_4</Hit_accession>
-          <Hit_len>983</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>658.197981896696</Hsp_bit-score>
-              <Hsp_score>1517</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>11</Hsp_query-from>
-              <Hsp_query-to>336</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>978</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>1</Hsp_hit-frame>
-              <Hsp_identity>310</Hsp_identity>
-              <Hsp_positive>322</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>326</Hsp_align-len>
-              <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT</Hsp_qseq>
-              <Hsp_hseq>VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT</Hsp_hseq>
-              <Hsp_midline>VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>23</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_5</Hit_id>
-          <Hit_def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Hit_def>
-          <Hit_accession>Subject_5</Hit_accession>
-          <Hit_len>1047</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>711.255977415469</Hsp_bit-score>
-              <Hsp_score>1640</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>348</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>1044</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>1</Hsp_hit-frame>
-              <Hsp_identity>325</Hsp_identity>
-              <Hsp_positive>337</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>348</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT   E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>24</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_6</Hit_id>
-          <Hit_def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Hit_def>
-          <Hit_accession>Subject_6</Hit_accession>
-          <Hit_len>1344</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>626.708277239213</Hsp_bit-score>
-              <Hsp_score>1444</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>341</Hsp_query-to>
-              <Hsp_hit-from>23</Hsp_hit-from>
-              <Hsp_hit-to>1048</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>2</Hsp_hit-frame>
-              <Hsp_identity>281</Hsp_identity>
-              <Hsp_positive>311</Hsp_positive>
-              <Hsp_gaps>1</Hsp_gaps>
-              <Hsp_align-len>342</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE HAIMGV  TW MALACA PPL GWSRYIPEGLQCSCGIDYYT  P +NNESFVIYMF  HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR CM+TT+CCGKNP   +D ASAT SKTE</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-  </BlastOutput_iterations>
-</BlastOutput>
diff --git a/test-data/tblastn_four_human_vs_rhodopsin.xml b/test-data/tblastn_four_human_vs_rhodopsin.xml
deleted file mode 100644
index 9bccf112f2d..00000000000
--- a/test-data/tblastn_four_human_vs_rhodopsin.xml
+++ /dev/null
@@ -1,722 +0,0 @@
-<?xml version="1.0"?>
-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
-<BlastOutput>
-  <BlastOutput_program>tblastn</BlastOutput_program>
-  <BlastOutput_version>TBLASTN 2.2.25+</BlastOutput_version>
-  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
-  <BlastOutput_db></BlastOutput_db>
-  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
-  <BlastOutput_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</BlastOutput_query-def>
-  <BlastOutput_query-len>406</BlastOutput_query-len>
-  <BlastOutput_param>
-    <Parameters>
-      <Parameters_matrix>BLOSUM80</Parameters_matrix>
-      <Parameters_expect>1e-10</Parameters_expect>
-      <Parameters_gap-open>10</Parameters_gap-open>
-      <Parameters_gap-extend>1</Parameters_gap-extend>
-      <Parameters_filter>F</Parameters_filter>
-    </Parameters>
-  </BlastOutput_param>
-  <BlastOutput_iterations>
-    <Iteration>
-      <Iteration_iter-num>1</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>2</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>3</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>4</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>5</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>6</Iteration_iter-num>
-      <Iteration_query-ID>Query_1</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>19</Statistics_hsp-len>
-          <Statistics_eff-space>127710</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>7</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>8</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>9</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>10</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>11</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>12</Iteration_iter-num>
-      <Iteration_query-ID>Query_2</Iteration_query-ID>
-      <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>23</Statistics_hsp-len>
-          <Statistics_eff-space>370988</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>13</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>14</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>15</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>16</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>17</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>18</Iteration_iter-num>
-      <Iteration_query-ID>Query_3</Iteration_query-ID>
-      <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>24</Statistics_hsp-len>
-          <Statistics_eff-space>441350</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>19</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_1</Hit_id>
-          <Hit_def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Hit_def>
-          <Hit_accession>Subject_1</Hit_accession>
-          <Hit_len>1047</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>732.392902459534</Hsp_bit-score>
-              <Hsp_score>1689</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>348</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>1044</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>1</Hsp_hit-frame>
-              <Hsp_identity>336</Hsp_identity>
-              <Hsp_positive>343</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>348</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>20</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_2</Hit_id>
-          <Hit_def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Hit_def>
-          <Hit_accession>Subject_2</Hit_accession>
-          <Hit_len>1574</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>646.119739014374</Hsp_bit-score>
-              <Hsp_score>1489</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>341</Hsp_query-to>
-              <Hsp_hit-from>42</Hsp_hit-from>
-              <Hsp_hit-to>1067</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>3</Hsp_hit-frame>
-              <Hsp_identity>290</Hsp_identity>
-              <Hsp_positive>320</Hsp_positive>
-              <Hsp_gaps>1</Hsp_gaps>
-              <Hsp_align-len>342</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S+ GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF+ QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA  SKTE</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>21</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_3</Hit_id>
-          <Hit_def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Hit_def>
-          <Hit_accession>Subject_3</Hit_accession>
-          <Hit_len>4301</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>151.343146656381</Hsp_bit-score>
-              <Hsp_score>342</Hsp_score>
-              <Hsp_evalue>1.39566684546685e-72</Hsp_evalue>
-              <Hsp_query-from>239</Hsp_query-from>
-              <Hsp_query-to>312</Hsp_query-to>
-              <Hsp_hit-from>3147</Hsp_hit-from>
-              <Hsp_hit-to>3368</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>3</Hsp_hit-frame>
-              <Hsp_identity>69</Hsp_identity>
-              <Hsp_positive>73</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>74</Hsp_align-len>
-              <Hsp_qseq>ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ</Hsp_qseq>
-              <Hsp_hseq>ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ</Hsp_hseq>
-              <Hsp_midline>ESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQ</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>2</Hsp_num>
-              <Hsp_bit-score>126.323929257285</Hsp_bit-score>
-              <Hsp_score>284</Hsp_score>
-              <Hsp_evalue>1.39566684546685e-72</Hsp_evalue>
-              <Hsp_query-from>177</Hsp_query-from>
-              <Hsp_query-to>235</Hsp_query-to>
-              <Hsp_hit-from>2855</Hsp_hit-from>
-              <Hsp_hit-to>3031</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>2</Hsp_hit-frame>
-              <Hsp_identity>54</Hsp_identity>
-              <Hsp_positive>57</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>59</Hsp_align-len>
-              <Hsp_qseq>RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA</Hsp_qseq>
-              <Hsp_hseq>RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS</Hsp_hseq>
-              <Hsp_midline>RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE  +</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>3</Hsp_num>
-              <Hsp_bit-score>229.420359574251</Hsp_bit-score>
-              <Hsp_score>523</Hsp_score>
-              <Hsp_evalue>9.84654801241353e-65</Hsp_evalue>
-              <Hsp_query-from>11</Hsp_query-from>
-              <Hsp_query-to>121</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>333</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>1</Hsp_hit-frame>
-              <Hsp_identity>107</Hsp_identity>
-              <Hsp_positive>109</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>111</Hsp_align-len>
-              <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_qseq>
-              <Hsp_hseq>VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_hseq>
-              <Hsp_midline>VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>4</Hsp_num>
-              <Hsp_bit-score>122.873002719478</Hsp_bit-score>
-              <Hsp_score>276</Hsp_score>
-              <Hsp_evalue>1.40732096096596e-32</Hsp_evalue>
-              <Hsp_query-from>119</Hsp_query-from>
-              <Hsp_query-to>177</Hsp_query-to>
-              <Hsp_hit-from>1404</Hsp_hit-from>
-              <Hsp_hit-to>1580</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>3</Hsp_hit-frame>
-              <Hsp_identity>55</Hsp_identity>
-              <Hsp_positive>56</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>59</Hsp_align-len>
-              <Hsp_qseq>LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR</Hsp_qseq>
-              <Hsp_hseq>LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR</Hsp_hseq>
-              <Hsp_midline>L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR</Hsp_midline>
-            </Hsp>
-            <Hsp>
-              <Hsp_num>5</Hsp_num>
-              <Hsp_bit-score>57.7367643183824</Hsp_bit-score>
-              <Hsp_score>125</Hsp_score>
-              <Hsp_evalue>5.60065526485586e-13</Hsp_evalue>
-              <Hsp_query-from>312</Hsp_query-from>
-              <Hsp_query-to>337</Hsp_query-to>
-              <Hsp_hit-from>4222</Hsp_hit-from>
-              <Hsp_hit-to>4299</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>1</Hsp_hit-frame>
-              <Hsp_identity>23</Hsp_identity>
-              <Hsp_positive>24</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>26</Hsp_align-len>
-              <Hsp_qseq>QFRNCMLTTICCGKNPLGDDEASATV</Hsp_qseq>
-              <Hsp_hseq>QFRNCMLTTLCCGKNPLGDDEASTTA</Hsp_hseq>
-              <Hsp_midline>QFRNCMLTT+CCGKNPLGDDEAS T </Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>22</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_4</Hit_id>
-          <Hit_def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Hit_def>
-          <Hit_accession>Subject_4</Hit_accession>
-          <Hit_len>983</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>658.197981896696</Hsp_bit-score>
-              <Hsp_score>1517</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>11</Hsp_query-from>
-              <Hsp_query-to>336</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>978</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>1</Hsp_hit-frame>
-              <Hsp_identity>310</Hsp_identity>
-              <Hsp_positive>322</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>326</Hsp_align-len>
-              <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT</Hsp_qseq>
-              <Hsp_hseq>VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT</Hsp_hseq>
-              <Hsp_midline>VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>23</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_5</Hit_id>
-          <Hit_def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Hit_def>
-          <Hit_accession>Subject_5</Hit_accession>
-          <Hit_len>1047</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>711.255977415469</Hsp_bit-score>
-              <Hsp_score>1640</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>348</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>1044</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>1</Hsp_hit-frame>
-              <Hsp_identity>325</Hsp_identity>
-              <Hsp_positive>337</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>348</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT   E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>24</Iteration_iter-num>
-      <Iteration_query-ID>Query_4</Iteration_query-ID>
-      <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>Subject_6</Hit_id>
-          <Hit_def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Hit_def>
-          <Hit_accession>Subject_6</Hit_accession>
-          <Hit_len>1344</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>626.708277239213</Hsp_bit-score>
-              <Hsp_score>1444</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>341</Hsp_query-to>
-              <Hsp_hit-from>23</Hsp_hit-from>
-              <Hsp_hit-to>1048</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>2</Hsp_hit-frame>
-              <Hsp_identity>281</Hsp_identity>
-              <Hsp_positive>311</Hsp_positive>
-              <Hsp_gaps>1</Hsp_gaps>
-              <Hsp_align-len>342</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE HAIMGV  TW MALACA PPL GWSRYIPEGLQCSCGIDYYT  P +NNESFVIYMF  HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR CM+TT+CCGKNP   +D ASAT SKTE</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>18</Statistics_hsp-len>
-          <Statistics_eff-space>109230</Statistics_eff-space>
-          <Statistics_kappa>0.071</Statistics_kappa>
-          <Statistics_lambda>0.299</Statistics_lambda>
-          <Statistics_entropy>0.27</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-  </BlastOutput_iterations>
-</BlastOutput>
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 17a4b5421d9..d9eafeba58c 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -244,14 +244,6 @@
     <tool file="fastx_toolkit/fasta_nucleotide_changer.xml" />
     <tool file="fastx_toolkit/fastx_collapser.xml" />
   </section>
-  <section name="NCBI BLAST+" id="ncbi_blast_plus_tools">
-    <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" />
-    <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" />
-    <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" />
-    <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" />
-    <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" />
-    <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" />
-  </section>
   <section name="NGS: QC and manipulation" id="NGS_QC">
     
     <label text="FastQC: fastq/sam/bam" id="fastqcsambam" />
diff --git a/tools/ncbi_blast_plus/blastxml_to_tabular.py b/tools/ncbi_blast_plus/blastxml_to_tabular.py
deleted file mode 100644
index 7098fec2d2b..00000000000
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.py
+++ /dev/null
@@ -1,254 +0,0 @@
-#!/usr/bin/env python
-"""Convert a BLAST XML file to 12 column tabular output
-
-Takes three command line options, input BLAST XML filename, output tabular
-BLAST filename, output format (std for standard 12 columns, or ext for the
-extended 24 columns offered in the BLAST+ wrappers).
-
-The 12 columns output are 'qseqid sseqid pident length mismatch gapopen qstart
-qend sstart send evalue bitscore' or 'std' at the BLAST+ command line, which
-mean:
-   
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
-     1 qseqid    Query Seq-id (ID of your sequence)
-     2 sseqid    Subject Seq-id (ID of the database hit)
-     3 pident    Percentage of identical matches
-     4 length    Alignment length
-     5 mismatch  Number of mismatches
-     6 gapopen   Number of gap openings
-     7 qstart    Start of alignment in query
-     8 qend      End of alignment in query
-     9 sstart    Start of alignment in subject (database hit)
-    10 send      End of alignment in subject (database hit)
-    11 evalue    Expectation value (E-value)
-    12 bitscore  Bit score
-====== ========= ============================================
-
-The additional columns offered in the Galaxy BLAST+ wrappers are:
-
-====== ============= ===========================================
-Column NCBI name     Description
------- ------------- -------------------------------------------
-    13 sallseqid     All subject Seq-id(s), separated by a ';'
-    14 score         Raw score
-    15 nident        Number of identical matches
-    16 positive      Number of positive-scoring matches
-    17 gaps          Total number of gaps
-    18 ppos          Percentage of positive-scoring matches
-    19 qframe        Query frame
-    20 sframe        Subject frame
-    21 qseq          Aligned part of query sequence
-    22 sseq          Aligned part of subject sequence
-    23 qlen          Query sequence length
-    24 slen          Subject sequence length
-====== ============= ===========================================
-
-Most of these fields are given explicitly in the XML file, others some like
-the percentage identity and the number of gap openings must be calculated.
-
-Be aware that the sequence in the extended tabular output or XML direct from
-BLAST+ may or may not use XXXX masking on regions of low complexity. This
-can throw the off the calculation of percentage identity and gap openings.
-[In fact, both BLAST 2.2.24+ and 2.2.25+ have a subtle bug in this regard,
-with these numbers changing depending on whether or not the low complexity
-filter is used.]
-
-This script attempts to produce identical output to what BLAST+ would have done.
-However, check this with "diff -b ..." since BLAST+ sometimes includes an extra
-space character (probably a bug).
-"""
-import sys
-import re
-
-if sys.version_info[:2] >= ( 2, 5 ):
-    import xml.etree.cElementTree as ElementTree
-else:
-    from galaxy import eggs
-    import pkg_resources; pkg_resources.require( "elementtree" )
-    from elementtree import ElementTree
-
-def stop_err( msg ):
-    sys.stderr.write("%s\n" % msg)
-    sys.exit(1)
-
-#Parse Command Line
-try:
-    in_file, out_file, out_fmt = sys.argv[1:]
-except:
-    stop_err("Expect 3 arguments: input BLAST XML file, output tabular file, out format (std or ext)")
-
-if out_fmt == "std":
-    extended = False
-elif out_fmt == "x22":
-    stop_err("Format argument x22 has been replaced with ext (extended 24 columns)")
-elif out_fmt == "ext":
-    extended = True
-else:
-    stop_err("Format argument should be std (12 column) or ext (extended 24 columns)")
-
-
-# get an iterable
-try: 
-    context = ElementTree.iterparse(in_file, events=("start", "end"))
-except:
-    stop_err("Invalid data format.")
-# turn it into an iterator
-context = iter(context)
-# get the root element
-try:
-    event, root = context.next()
-except:
-    stop_err( "Invalid data format." )
-
-
-re_default_query_id = re.compile("^Query_\d+$")
-assert re_default_query_id.match("Query_101")
-assert not re_default_query_id.match("Query_101a")
-assert not re_default_query_id.match("MyQuery_101")
-re_default_subject_id = re.compile("^Subject_\d+$")
-assert re_default_subject_id.match("Subject_1")
-assert not re_default_subject_id.match("Subject_")
-assert not re_default_subject_id.match("Subject_12a")
-assert not re_default_subject_id.match("TheSubject_1")
-
-
-outfile = open(out_file, 'w')
-blast_program = None
-for event, elem in context:
-    if event == "end" and elem.tag == "BlastOutput_program":
-        blast_program = elem.text
-    # for every <Iteration> tag
-    if event == "end" and elem.tag == "Iteration":
-        #Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA
-        # <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-        # <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-        # <Iteration_query-len>406</Iteration_query-len>
-        # <Iteration_hits></Iteration_hits>
-        #
-        #Or, from BLAST 2.2.24+ run online
-        # <Iteration_query-ID>Query_1</Iteration_query-ID>
-        # <Iteration_query-def>Sample</Iteration_query-def>
-        # <Iteration_query-len>516</Iteration_query-len>
-        # <Iteration_hits>...
-        qseqid = elem.findtext("Iteration_query-ID")
-        if re_default_query_id.match(qseqid):
-            #Place holder ID, take the first word of the query definition
-            qseqid = elem.findtext("Iteration_query-def").split(None,1)[0]
-        qlen = int(elem.findtext("Iteration_query-len"))
-                                        
-        # for every <Hit> within <Iteration>
-        for hit in elem.findall("Iteration_hits/Hit"):
-            #Expecting either this,
-            # <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id>
-            # <Hit_def>RecName: Full=Rhodopsin</Hit_def>
-            # <Hit_accession>P56514</Hit_accession>
-            #or,
-            # <Hit_id>Subject_1</Hit_id>
-            # <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def>
-            # <Hit_accession>Subject_1</Hit_accession>
-            #
-            #apparently depending on the parse_deflines switch
-            sseqid = hit.findtext("Hit_id").split(None,1)[0]
-            hit_def = sseqid + " " + hit.findtext("Hit_def")
-            if re_default_subject_id.match(sseqid) \
-            and sseqid == hit.findtext("Hit_accession"):
-                #Place holder ID, take the first word of the subject definition
-                hit_def = hit.findtext("Hit_def")
-                sseqid = hit_def.split(None,1)[0]
-            # for every <Hsp> within <Hit>
-            for hsp in hit.findall("Hit_hsps/Hsp"):
-                nident = hsp.findtext("Hsp_identity")
-                length = hsp.findtext("Hsp_align-len")
-                pident = "%0.2f" % (100*float(nident)/float(length))
-
-                q_seq = hsp.findtext("Hsp_qseq")
-                h_seq = hsp.findtext("Hsp_hseq")
-                m_seq = hsp.findtext("Hsp_midline")
-                assert len(q_seq) == len(h_seq) == len(m_seq) == int(length)
-                gapopen = str(len(q_seq.replace('-', ' ').split())-1  + \
-                              len(h_seq.replace('-', ' ').split())-1)
-
-                mismatch = m_seq.count(' ') + m_seq.count('+') \
-                         - q_seq.count('-') - h_seq.count('-')
-                #TODO - Remove this alternative mismatch calculation and test
-                #once satisifed there are no problems
-                expected_mismatch = len(q_seq) \
-                                  - sum(1 for q,h in zip(q_seq, h_seq) \
-                                        if q == h or q == "-" or h == "-")
-                xx = sum(1 for q,h in zip(q_seq, h_seq) if q=="X" and h=="X")
-                if not (expected_mismatch - q_seq.count("X") <= int(mismatch) <= expected_mismatch + xx):
-                    stop_err("%s vs %s mismatches, expected %i <= %i <= %i" \
-                             % (qseqid, sseqid, expected_mismatch - q_seq.count("X"),
-                                int(mismatch), expected_mismatch))
-
-                #TODO - Remove this alternative identity calculation and test
-                #once satisifed there are no problems
-                expected_identity = sum(1 for q,h in zip(q_seq, h_seq) if q == h)
-                if not (expected_identity - xx <= int(nident) <= expected_identity + q_seq.count("X")):
-                    stop_err("%s vs %s identities, expected %i <= %i <= %i" \
-                             % (qseqid, sseqid, expected_identity, int(nident),
-                                expected_identity + q_seq.count("X")))
-                
-
-                evalue = hsp.findtext("Hsp_evalue")
-                if evalue == "0":
-                    evalue = "0.0"
-                else:
-                    evalue = "%0.0e" % float(evalue)
-                
-                bitscore = float(hsp.findtext("Hsp_bit-score"))
-                if bitscore < 100:
-                    #Seems to show one decimal place for lower scores
-                    bitscore = "%0.1f" % bitscore
-                else:
-                    #Note BLAST does not round to nearest int, it truncates
-                    bitscore = "%i" % bitscore
-
-                values = [qseqid,
-                          sseqid,
-                          pident,
-                          length, #hsp.findtext("Hsp_align-len")
-                          str(mismatch),
-                          gapopen,
-                          hsp.findtext("Hsp_query-from"), #qstart,
-                          hsp.findtext("Hsp_query-to"), #qend,
-                          hsp.findtext("Hsp_hit-from"), #sstart,
-                          hsp.findtext("Hsp_hit-to"), #send,
-                          evalue, #hsp.findtext("Hsp_evalue") in scientific notation
-                          bitscore, #hsp.findtext("Hsp_bit-score") rounded
-                          ]
-
-                if extended:
-                    sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(">"))
-                    #print hit_def, "-->", sallseqid
-                    positive = hsp.findtext("Hsp_positive")
-                    ppos = "%0.2f" % (100*float(positive)/float(length))
-                    qframe = hsp.findtext("Hsp_query-frame")
-                    sframe = hsp.findtext("Hsp_hit-frame")
-                    if blast_program == "blastp":
-                        #Probably a bug in BLASTP that they use 0 or 1 depending on format
-                        if qframe == "0": qframe = "1"
-                        if sframe == "0": sframe = "1"
-                    slen = int(hit.findtext("Hit_len"))
-                    values.extend([sallseqid,
-                                   hsp.findtext("Hsp_score"), #score,
-                                   nident,
-                                   positive,
-                                   hsp.findtext("Hsp_gaps"), #gaps,
-                                   ppos,
-                                   qframe,
-                                   sframe,
-                                   #NOTE - for blastp, XML shows original seq, tabular uses XXX masking
-                                   q_seq,
-                                   h_seq,
-                                   str(qlen),
-                                   str(slen),
-                                   ])
-                #print "\t".join(values) 
-                outfile.write("\t".join(values) + "\n")
-        # prevents ElementTree from growing large datastructure
-        root.clear()
-        elem.clear()
-outfile.close()
diff --git a/tools/ncbi_blast_plus/blastxml_to_tabular.xml b/tools/ncbi_blast_plus/blastxml_to_tabular.xml
deleted file mode 100644
index 66bba2c06fc..00000000000
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml
+++ /dev/null
@@ -1,127 +0,0 @@
-<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.8">
-    <description>Convert BLAST XML output to tabular</description>
-    <command interpreter="python">
-      blastxml_to_tabular.py $blastxml_file $tabular_file $out_format
-    </command>
-    <inputs>
-        <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> 
-        <param name="out_format" type="select" label="Output format">
-            <option value="std" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
-        </param>
-    </inputs>
-    <outputs>
-        <data name="tabular_file" format="tabular" label="BLAST results as tabular" />
-    </outputs>
-    <requirements>
-    </requirements>
-    <tests>
-        <test>
-            <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
-            <param name="out_format" value="std" />
-            <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin.tabluar -->
-            <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
-            <param name="out_format" value="ext" />
-            <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin_22c.tabluar -->
-            <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted_ext.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="blastxml_file" value="blastp_sample.xml" ftype="blastxml" />
-            <param name="out_format" value="std" />
-            <!-- Note this has some white space differences from the actual blastp output -->
-            <output name="tabular_file" file="blastp_sample_converted.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" />
-            <param name="out_format" value="std" />
-            <!-- Note this has some white space differences from the actual blastx output -->
-            <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" />
-            <param name="out_format" value="ext" />
-            <!-- Note this has some white space and XXXX masking differences from the actual blastx output -->
-            <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted_ext.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="blastxml_file" value="blastx_sample.xml" ftype="blastxml" />
-            <param name="out_format" value="std" />
-            <!-- Note this has some white space differences from the actual blastx output -->
-            <output name="tabular_file" file="blastx_sample_converted.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" />
-            <param name="out_format" value="std" />
-            <!-- Note this has some white space differences from the actual blastp output -->
-            <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_std.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" />
-            <param name="out_format" value="ext" />
-            <!-- Note this has some white space differences from the actual blastp output -->
-            <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" />
-        </test>
-    </tests>
-    <help>
-    
-**What it does**
-
-NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of
-formats including tabular and a more detailed XML format. A complex workflow
-may need both the XML and the tabular output - but running BLAST twice is
-slow and wasteful.
-
-This tool takes the BLAST XML output and by default converts it into the
-standard 12 column tabular equivalent:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
-     1 qseqid    Query Seq-id (ID of your sequence)
-     2 sseqid    Subject Seq-id (ID of the database hit)
-     3 pident    Percentage of identical matches
-     4 length    Alignment length
-     5 mismatch  Number of mismatches
-     6 gapopen   Number of gap openings
-     7 qstart    Start of alignment in query
-     8 qend      End of alignment in query
-     9 sstart    Start of alignment in subject (database hit)
-    10 send      End of alignment in subject (database hit)
-    11 evalue    Expectation value (E-value)
-    12 bitscore  Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 22 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name     Description
------- ------------- -------------------------------------------
-    13 sallseqid     All subject Seq-id(s), separated by a ';'
-    14 score         Raw score
-    15 nident        Number of identical matches
-    16 positive      Number of positive-scoring matches
-    17 gaps          Total number of gaps
-    18 ppos          Percentage of positive-scoring matches
-    19 qframe        Query frame
-    20 sframe        Subject frame
-    21 qseq          Aligned part of query sequence
-    22 sseq          Aligned part of subject sequence
-    23 qlen          Query sequence length
-    24 slen          Subject sequence length
-====== ============= ===========================================
-
-Beware that the XML file (and thus the conversion) and the tabular output
-direct from BLAST+ may differ in the presence of XXXX masking on regions
-low complexity (columns 21 and 22), and thus also calculated figures like
-the percentage idenity (column 3).
-
-    </help>
-</tool>
diff --git a/tools/ncbi_blast_plus/hide_stderr.py b/tools/ncbi_blast_plus/hide_stderr.py
deleted file mode 100755
index ebb49d36f29..00000000000
--- a/tools/ncbi_blast_plus/hide_stderr.py
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/usr/bin/env python
-"""A simple script to redirect stderr to stdout when the return code is zero.
-
-See https://bitbucket.org/galaxy/galaxy-central/issue/325/
-
-Currently Galaxy ignores the return code from command line tools (even if it
-is non-zero which by convention indicates an error) and treats any output on
-stderr as an error (even though by convention stderr is used for errors or
-warnings).
-
-This script runs the given command line, capturing all stdout and stderr in
-memory, and gets the return code. For a zero return code, any stderr (which
-should be warnings only) is added to the stdout. That way Galaxy believes
-everything is fine. For a non-zero return code, we output stdout as is, and
-any stderr, plus the return code to ensure there is some output on stderr.
-That way Galaxy treats this as an error.
-
-Once issue 325 is fixed, this script will not be needed.
-"""
-import sys
-import subprocess
-
-#Avoid using shell=True when we call subprocess to ensure if the Python
-#script is killed, so too is the BLAST process.
-try:
-    words = []
-    for w in sys.argv[1:]:
-       if " " in w:
-           words.append('"%s"' % w)
-       else:
-           words.append(w)
-    cmd = " ".join(words)
-    child = subprocess.Popen(sys.argv[1:],
-                             stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-except Exception, err:
-    sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
-    sys.exit(1)
-#Use .communicate as can get deadlocks with .wait(),
-stdout, stderr = child.communicate()
-return_code = child.returncode
-
-if return_code:
-    sys.stdout.write(stdout)
-    sys.stderr.write(stderr)
-    sys.stderr.write("Return error code %i from command:\n" % return_code)
-    sys.stderr.write("%s\n" % cmd)
-else:
-    sys.stdout.write(stdout)
-    sys.stdout.write(stderr)
diff --git a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
deleted file mode 100644
index 6b942380403..00000000000
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
+++ /dev/null
@@ -1,211 +0,0 @@
-<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.11">
-    <description>Search nucleotide database with nucleotide query sequence(s)</description>
-    <!-- If job splitting is enabled, break up the query file into four -->
-    <parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism>
-    <version_command>blastn -version</version_command>
-    <command interpreter="python">hide_stderr.py
-## The command is a Cheetah template which allows some Python based syntax.
-## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
-blastn
--query "$query"
-#if $db_opts.db_opts_selector == "db":
-  -db "${db_opts.database.fields.path}"
-#else:
-  -subject "$db_opts.subject"
-#end if
--task $blast_type
--evalue $evalue_cutoff
--out $output1
-##Set the extended list here so if/when we add things, saved workflows are not affected
-#if str($out_format)=="ext":
-    -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
-#else:
-    -outfmt $out_format
-#end if
--num_threads 8
-#if $adv_opts.adv_opts_selector=="advanced":
-$adv_opts.filter_query
-$adv_opts.strand
-## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
-## Note -max_target_seqs overrides -num_descriptions and -num_alignments
-#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
--max_target_seqs $adv_opts.max_hits
-#end if
-#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
--word_size $adv_opts.word_size
-#end if
-$adv_opts.ungapped
-$adv_opts.parse_deflines
-## End of advanced options:
-#end if
-    </command>
-    <inputs>
-        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
-        <conditional name="db_opts">
-            <param name="db_opts_selector" type="select" label="Subject database/sequences">
-              <option value="db" selected="True">BLAST Database</option>
-              <option value="file">FASTA file</option>
-            </param>
-            <when value="db">
-                <param name="database" type="select" label="Nucleotide BLAST database">
-                    <options from_file="blastdb.loc">
-                      <column name="value" index="0"/>
-                      <column name="name" index="1"/>
-                      <column name="path" index="2"/>
-                    </options>
-                </param>
-                <param name="subject" type="hidden" value="" /> 
-            </when>
-            <when value="file">
-                <param name="database" type="hidden" value="" /> 
-                <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> 
-            </when>
-        </conditional>
-        <param name="blast_type" type="select" display="radio" label="Type of BLAST">
-            <option value="megablast">megablast</option>
-            <option value="blastn">blastn</option>
-            <option value="blastn-short">blastn-short</option>
-            <option value="dc-megablast">dc-megablast</option>
-            <!-- Using BLAST 2.2.24+ this gives an error:
-            BLAST engine error: Program type 'vecscreen' not supported
-            <option value="vecscreen">vecscreen</option>
-            -->
-        </param>
-        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
-        <param name="out_format" type="select" label="Output format">
-            <option value="6" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
-            <option value="5">BLAST XML</option>
-            <option value="0">Pairwise text</option>
-            <option value="0 -html">Pairwise HTML</option>
-            <option value="2">Query-anchored text</option>
-            <option value="2 -html">Query-anchored HTML</option>
-            <option value="4">Flat query-anchored text</option>
-            <option value="4 -html">Flat query-anchored HTML</option>
-            <!--
-            <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
-            -->
-        </param>
-        <conditional name="adv_opts">
-            <param name="adv_opts_selector" type="select" label="Advanced Options">
-              <option value="basic" selected="True">Hide Advanced Options</option>
-              <option value="advanced">Show Advanced Options</option>
-            </param>
-            <when value="basic" />
-            <when value="advanced">
-                <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' -->
-                <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" />
-                <param name="strand" type="select" label="Query strand(s) to search against database/subject">
-                    <option value="-strand both">Both</option>
-                    <option value="-strand plus">Plus (forward)</option>
-                    <option value="-strand minus">Minus (reverse complement)</option>
-                </param>
-                <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
-                <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
-                    <validator type="in_range" min="0" />
-                </param>
-                <!-- I'd like word_size to be optional, with minimum 4 for blastn -->
-                <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4.">
-                    <validator type="in_range" min="0" />
-                </param>
-                <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
-                <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}">
-            <change_format>
-                <when input="out_format" value="0" format="txt"/>
-                <when input="out_format" value="0 -html" format="html"/>
-                <when input="out_format" value="2" format="txt"/>
-                <when input="out_format" value="2 -html" format="html"/>
-                <when input="out_format" value="4" format="txt"/>
-                <when input="out_format" value="4 -html" format="html"/>
-                <when input="out_format" value="5" format="blastxml"/>
-            </change_format>
-        </data>
-    </outputs>
-    <requirements>
-        <requirement type="binary">blastn</requirement>
-    </requirements>
-    <help>
-    
-.. class:: warningmark
-
-**Note**. Database searches may take a substantial amount of time.
-For large input datasets it is advisable to allow overnight processing.  
-
------
-
-**What it does**
-
-Search a *nucleotide database* using a *nucleotide query*,
-using the NCBI BLAST+ blastn command line tool.
-Algorithms include blastn, megablast, and discontiguous megablast.
-
------
-
-**Output format**
-
-Because Galaxy focuses on processing tabular data, the default output of this
-tool is tabular. The standard BLAST+ tabular output contains 12 columns:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
-     1 qseqid    Query Seq-id (ID of your sequence)
-     2 sseqid    Subject Seq-id (ID of the database hit)
-     3 pident    Percentage of identical matches
-     4 length    Alignment length
-     5 mismatch  Number of mismatches
-     6 gapopen   Number of gap openings
-     7 qstart    Start of alignment in query
-     8 qend      End of alignment in query
-     9 sstart    Start of alignment in subject (database hit)
-    10 send      End of alignment in subject (database hit)
-    11 evalue    Expectation value (E-value)
-    12 bitscore  Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name     Description
------- ------------- -------------------------------------------
-    13 sallseqid     All subject Seq-id(s), separated by a ';'
-    14 score         Raw score
-    15 nident        Number of identical matches
-    16 positive      Number of positive-scoring matches
-    17 gaps          Total number of gaps
-    18 ppos          Percentage of positive-scoring matches
-    19 qframe        Query frame
-    20 sframe        Subject frame
-    21 qseq          Aligned part of query sequence
-    22 sseq          Aligned part of subject sequence
-    23 qlen          Query sequence length
-    24 slen          Subject sequence length
-====== ============= ===========================================
-
-The third option is BLAST XML output, which is designed to be parsed by
-another program, and is understood by some Galaxy tools.
-
-You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
-The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
-The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
-The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
-and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
-
--------
-
-**References**
-
-Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214.
-
-    </help>
-</tool>
diff --git a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
deleted file mode 100644
index 17dda06e5e1..00000000000
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
+++ /dev/null
@@ -1,278 +0,0 @@
-<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.11">
-    <description>Search protein database with protein query sequence(s)</description>
-    <!-- If job splitting is enabled, break up the query file into four -->
-    <parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism>
-    <version_command>blastp -version</version_command>
-    <command interpreter="python">hide_stderr.py
-## The command is a Cheetah template which allows some Python based syntax.
-## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
-blastp
--query "$query"
-#if $db_opts.db_opts_selector == "db":
-  -db "${db_opts.database.fields.path}"
-#else:
-  -subject "$db_opts.subject"
-#end if
--task $blast_type
--evalue $evalue_cutoff
--out $output1
-##Set the extended list here so if/when we add things, saved workflows are not affected
-#if str($out_format)=="ext":
-    -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
-#else:
-    -outfmt $out_format
-#end if
--num_threads 8
-#if $adv_opts.adv_opts_selector=="advanced":
-$adv_opts.filter_query
--matrix $adv_opts.matrix
-## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
-## Note -max_target_seqs overrides -num_descriptions and -num_alignments
-#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
--max_target_seqs $adv_opts.max_hits
-#end if
-#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
--word_size $adv_opts.word_size
-#end if
-##Ungapped disabled for now - see comments below
-##$adv_opts.ungapped
-$adv_opts.parse_deflines
-## End of advanced options:
-#end if
-    </command>
-    <inputs>
-        <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 
-        <conditional name="db_opts">
-            <param name="db_opts_selector" type="select" label="Subject database/sequences">
-              <option value="db" selected="True">BLAST Database</option>
-              <option value="file">FASTA file</option>
-            </param>
-            <when value="db">
-                <param name="database" type="select" label="Protein BLAST database">
-                    <options from_file="blastdb_p.loc">
-                      <column name="value" index="0"/>
-                      <column name="name" index="1"/>
-                      <column name="path" index="2"/>
-                    </options>
-                </param>
-                <param name="subject" type="hidden" value="" /> 
-            </when>
-            <when value="file">
-                <param name="database" type="hidden" value="" /> 
-                <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> 
-            </when>
-        </conditional>
-        <param name="blast_type" type="select" display="radio" label="Type of BLAST">
-            <option value="blastp">blastp</option>
-            <option value="blastp-short">blastp-short</option>
-        </param>
-        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
-        <param name="out_format" type="select" label="Output format">
-            <option value="6" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
-            <option value="5">BLAST XML</option>
-            <option value="0">Pairwise text</option>
-            <option value="0 -html">Pairwise HTML</option>
-            <option value="2">Query-anchored text</option>
-            <option value="2 -html">Query-anchored HTML</option>
-            <option value="4">Flat query-anchored text</option>
-            <option value="4 -html">Flat query-anchored HTML</option>
-            <!--
-            <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
-            -->
-        </param>
-        <conditional name="adv_opts">
-            <param name="adv_opts_selector" type="select" label="Advanced Options">
-              <option value="basic" selected="True">Hide Advanced Options</option>
-              <option value="advanced">Show Advanced Options</option>
-            </param>
-            <when value="basic" />
-            <when value="advanced">
-                <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
-                <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" />
-                <param name="matrix" type="select" label="Scoring matrix">
-                    <option value="BLOSUM90">BLOSUM90</option>
-                    <option value="BLOSUM80">BLOSUM80</option>
-                    <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
-                    <option value="BLOSUM50">BLOSUM50</option> 
-                    <option value="BLOSUM45">BLOSUM45</option>
-                    <option value="PAM250">PAM250</option>
-                    <option value="PAM70">PAM70</option>
-                    <option value="PAM30">PAM30</option>
-                </param>
-                <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
-                <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
-                    <validator type="in_range" min="0" />
-                </param>
-                <!-- I'd like word_size to be optional, with minimum 2 for blastp -->
-                <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
-                    <validator type="in_range" min="0" />
-                </param>
-                <!--
-                Can't use '-ungapped' on its own, error back is:
-                Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search
-                Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.'
-                <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
-                -->
-                <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}">
-            <change_format>
-                <when input="out_format" value="0" format="txt"/>
-                <when input="out_format" value="0 -html" format="html"/>
-                <when input="out_format" value="2" format="txt"/>
-                <when input="out_format" value="2 -html" format="html"/>
-                <when input="out_format" value="4" format="txt"/>
-                <when input="out_format" value="4 -html" format="html"/>
-                <when input="out_format" value="5" format="blastxml"/>
-            </change_format>
-        </data>
-    </outputs>
-    <requirements>
-        <requirement type="binary">blastp</requirement>
-    </requirements>
-    <tests>
-        <test>
-            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-8" />
-            <param name="blast_type" value="blastp" />
-            <param name="out_format" value="5" />
-            <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="False" />
-            <param name="matrix" value="BLOSUM62" />
-            <param name="max_hits" value="0" />
-            <param name="word_size" value="0" />
-            <param name="parse_deflines" value="True" />
-            <output name="output1" file="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
-        </test>
-        <test>
-            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-8" />
-            <param name="blast_type" value="blastp" />
-            <param name="out_format" value="6" />
-            <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="False" />
-            <param name="matrix" value="BLOSUM62" />
-            <param name="max_hits" value="0" />
-            <param name="word_size" value="0" />
-            <param name="parse_deflines" value="True" />
-            <output name="output1" file="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-8" />
-            <param name="blast_type" value="blastp" />
-            <param name="out_format" value="ext" />
-            <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="False" />
-            <param name="matrix" value="BLOSUM62" />
-            <param name="max_hits" value="0" />
-            <param name="word_size" value="0" />
-            <param name="parse_deflines" value="True" />
-            <output name="output1" file="blastp_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-8" />
-            <param name="blast_type" value="blastp" />
-            <param name="out_format" value="6" />
-            <param name="adv_opts_selector" value="basic" />
-            <output name="output1" file="blastp_rhodopsin_vs_four_human.tabular" ftype="tabular" />
-        </test>
-    </tests>
-    <help>
-    
-.. class:: warningmark
-
-**Note**. Database searches may take a substantial amount of time.
-For large input datasets it is advisable to allow overnight processing.  
-
------
-
-**What it does**
-
-Search a *protein database* using a *protein query*,
-using the NCBI BLAST+ blastp command line tool.
-
------
-
-**Output format**
-
-Because Galaxy focuses on processing tabular data, the default output of this
-tool is tabular. The standard BLAST+ tabular output contains 12 columns:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
-     1 qseqid    Query Seq-id (ID of your sequence)
-     2 sseqid    Subject Seq-id (ID of the database hit)
-     3 pident    Percentage of identical matches
-     4 length    Alignment length
-     5 mismatch  Number of mismatches
-     6 gapopen   Number of gap openings
-     7 qstart    Start of alignment in query
-     8 qend      End of alignment in query
-     9 sstart    Start of alignment in subject (database hit)
-    10 send      End of alignment in subject (database hit)
-    11 evalue    Expectation value (E-value)
-    12 bitscore  Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name     Description
------- ------------- -------------------------------------------
-    13 sallseqid     All subject Seq-id(s), separated by a ';'
-    14 score         Raw score
-    15 nident        Number of identical matches
-    16 positive      Number of positive-scoring matches
-    17 gaps          Total number of gaps
-    18 ppos          Percentage of positive-scoring matches
-    19 qframe        Query frame
-    20 sframe        Subject frame
-    21 qseq          Aligned part of query sequence
-    22 sseq          Aligned part of subject sequence
-    23 qlen          Query sequence length
-    24 slen          Subject sequence length
-====== ============= ===========================================
-
-The third option is BLAST XML output, which is designed to be parsed by
-another program, and is understood by some Galaxy tools.
-
-You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
-The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
-The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
-The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
-and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
-
--------
-
-**References**
-
-Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
-
-Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005.
-
-    </help>
-</tool>
diff --git a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
deleted file mode 100644
index 487c433ee1b..00000000000
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
+++ /dev/null
@@ -1,242 +0,0 @@
-<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.11">
-    <description>Search protein database with translated nucleotide query sequence(s)</description>
-    <!-- If job splitting is enabled, break up the query file into four -->
-    <parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism>
-    <version_command>blastx -version</version_command>
-    <command interpreter="python">hide_stderr.py
-## The command is a Cheetah template which allows some Python based syntax.
-## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
-blastx
--query "$query"
-#if $db_opts.db_opts_selector == "db":
-  -db "${db_opts.database.fields.path}"
-#else:
-  -subject "$db_opts.subject"
-#end if
--evalue $evalue_cutoff
--out $output1
-##Set the extended list here so if/when we add things, saved workflows are not affected
-#if str($out_format)=="ext":
-    -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
-#else:
-    -outfmt $out_format
-#end if
--num_threads 8
-#if $adv_opts.adv_opts_selector=="advanced":
-$adv_opts.filter_query
-$adv_opts.strand
--matrix $adv_opts.matrix
-## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
-## Note -max_target_seqs overrides -num_descriptions and -num_alignments
-#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
--max_target_seqs $adv_opts.max_hits
-#end if
-#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
--word_size $adv_opts.word_size
-#end if
-$adv_opts.ungapped
-$adv_opts.parse_deflines
-## End of advanced options:
-#end if
-    </command>
-    <inputs>
-        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
-        <conditional name="db_opts">
-            <param name="db_opts_selector" type="select" label="Subject database/sequences">
-              <option value="db" selected="True">BLAST Database</option>
-              <option value="file">FASTA file</option>
-            </param>
-            <when value="db">
-                <param name="database" type="select" label="Protein BLAST database">
-                    <options from_file="blastdb_p.loc">
-                      <column name="value" index="0"/>
-                      <column name="name" index="1"/>
-                      <column name="path" index="2"/>
-                    </options>
-                </param>
-                <param name="subject" type="hidden" value="" /> 
-            </when>
-            <when value="file">
-                <param name="database" type="hidden" value="" /> 
-                <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> 
-            </when>
-        </conditional>
-        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
-        <param name="out_format" type="select" label="Output format">
-            <option value="6" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
-            <option value="5">BLAST XML</option>
-            <option value="0">Pairwise text</option>
-            <option value="0 -html">Pairwise HTML</option>
-            <option value="2">Query-anchored text</option>
-            <option value="2 -html">Query-anchored HTML</option>
-            <option value="4">Flat query-anchored text</option>
-            <option value="4 -html">Flat query-anchored HTML</option>
-            <!--
-            <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
-            -->
-        </param>
-        <conditional name="adv_opts">
-            <param name="adv_opts_selector" type="select" label="Advanced Options">
-              <option value="basic" selected="True">Hide Advanced Options</option>
-              <option value="advanced">Show Advanced Options</option>
-            </param>
-            <when value="basic" />
-            <when value="advanced">
-                <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
-                <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
-                <param name="strand" type="select" label="Query strand(s) to search against database/subject">
-                    <option value="-strand both">Both</option>
-                    <option value="-strand plus">Plus (forward)</option>
-                    <option value="-strand minus">Minus (reverse complement)</option>
-                </param>
-                <param name="matrix" type="select" label="Scoring matrix">
-                    <option value="BLOSUM90">BLOSUM90</option>
-                    <option value="BLOSUM80">BLOSUM80</option>
-                    <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
-                    <option value="BLOSUM50">BLOSUM50</option> 
-                    <option value="BLOSUM45">BLOSUM45</option>
-                    <option value="PAM250">PAM250</option>
-                    <option value="PAM70">PAM70</option>
-                    <option value="PAM30">PAM30</option>
-                </param>
-                <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
-                <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
-                    <validator type="in_range" min="0" />
-                </param>
-                <!-- I'd like word_size to be optional, with minimum 2 for blastx -->
-                <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
-                    <validator type="in_range" min="0" />
-                </param>
-                <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
-                <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="output1" format="tabular" label="blastx on ${db_opts.db_opts_selector}">
-            <change_format>
-                <when input="out_format" value="0" format="txt"/>
-                <when input="out_format" value="0 -html" format="html"/>
-                <when input="out_format" value="2" format="txt"/>
-                <when input="out_format" value="2 -html" format="html"/>
-                <when input="out_format" value="4" format="txt"/>
-                <when input="out_format" value="4 -html" format="html"/>
-                <when input="out_format" value="5" format="blastxml"/>
-            </change_format>
-        </data>
-    </outputs>
-    <requirements>
-        <requirement type="binary">blastx</requirement>
-    </requirements>
-    <tests>
-        <test>
-            <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-10" />
-            <param name="out_format" value="5" />
-            <param name="adv_opts_selector" value="basic" />
-            <output name="output1" file="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" />
-        </test>
-        <test>
-            <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-10" />
-            <param name="out_format" value="6" />
-            <param name="adv_opts_selector" value="basic" />
-            <output name="output1" file="blastx_rhodopsin_vs_four_human.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-10" />
-            <param name="out_format" value="ext" />
-            <param name="adv_opts_selector" value="basic" />
-            <output name="output1" file="blastx_rhodopsin_vs_four_human_ext.tabular" ftype="tabular" />
-        </test>
-    </tests>
-    <help>
-    
-.. class:: warningmark
-
-**Note**. Database searches may take a substantial amount of time.
-For large input datasets it is advisable to allow overnight processing.  
-
------
-
-**What it does**
-
-Search a *protein database* using a *translated nucleotide query*,
-using the NCBI BLAST+ blastx command line tool.
-
------
-
-**Output format**
-
-Because Galaxy focuses on processing tabular data, the default output of this
-tool is tabular. The standard BLAST+ tabular output contains 12 columns:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
-     1 qseqid    Query Seq-id (ID of your sequence)
-     2 sseqid    Subject Seq-id (ID of the database hit)
-     3 pident    Percentage of identical matches
-     4 length    Alignment length
-     5 mismatch  Number of mismatches
-     6 gapopen   Number of gap openings
-     7 qstart    Start of alignment in query
-     8 qend      End of alignment in query
-     9 sstart    Start of alignment in subject (database hit)
-    10 send      End of alignment in subject (database hit)
-    11 evalue    Expectation value (E-value)
-    12 bitscore  Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name     Description
------- ------------- -------------------------------------------
-    13 sallseqid     All subject Seq-id(s), separated by a ';'
-    14 score         Raw score
-    15 nident        Number of identical matches
-    16 positive      Number of positive-scoring matches
-    17 gaps          Total number of gaps
-    18 ppos          Percentage of positive-scoring matches
-    19 qframe        Query frame
-    20 sframe        Subject frame
-    21 qseq          Aligned part of query sequence
-    22 sseq          Aligned part of subject sequence
-    23 qlen          Query sequence length
-    24 slen          Subject sequence length 
-====== ============= ===========================================
-
-The third option is BLAST XML output, which is designed to be parsed by
-another program, and is understood by some Galaxy tools.
-
-You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
-The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
-The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
-The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
-and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
-
--------
-
-**References**
-
-Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
-
-    </help>
-</tool>
diff --git a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
deleted file mode 100644
index 73cead395d8..00000000000
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
+++ /dev/null
@@ -1,288 +0,0 @@
-<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.11">
-    <description>Search translated nucleotide database with protein query sequence(s)</description>
-    <!-- If job splitting is enabled, break up the query file into four -->
-    <parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism>
-    <version_command>tblastn -version</version_command>
-    <command interpreter="python">hide_stderr.py
-## The command is a Cheetah template which allows some Python based syntax.
-## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
-tblastn
--query "$query"
-#if $db_opts.db_opts_selector == "db":
-  -db "${db_opts.database.fields.path}"
-#else:
-  -subject "$db_opts.subject"
-#end if
--evalue $evalue_cutoff
--out $output1
-##Set the extended list here so if/when we add things, saved workflows are not affected
-#if str($out_format)=="ext":
-    -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
-#else:
-    -outfmt $out_format
-#end if
--num_threads 8
-#if $adv_opts.adv_opts_selector=="advanced":
-$adv_opts.filter_query
--matrix $adv_opts.matrix
-## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
-## Note -max_target_seqs overrides -num_descriptions and -num_alignments
-#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
--max_target_seqs $adv_opts.max_hits
-#end if
-#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
--word_size $adv_opts.word_size
-#end if
-##Ungapped disabled for now - see comments below
-##$adv_opts.ungapped
-$adv_opts.parse_deflines
-## End of advanced options:
-#end if
-    </command>
-    <inputs>
-        <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 
-        <conditional name="db_opts">
-            <param name="db_opts_selector" type="select" label="Subject database/sequences">
-              <option value="db" selected="True">BLAST Database</option>
-              <option value="file">FASTA file</option>
-            </param>
-            <when value="db">
-                <param name="database" type="select" label="Nucleotide BLAST database">
-                    <options from_file="blastdb.loc">
-                      <column name="value" index="0"/>
-                      <column name="name" index="1"/>
-                      <column name="path" index="2"/>
-                    </options>
-                </param>
-                <param name="subject" type="hidden" value="" /> 
-            </when>
-            <when value="file">
-                <param name="database" type="hidden" value="" /> 
-                <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> 
-            </when>
-        </conditional>
-        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
-        <param name="out_format" type="select" label="Output format">
-            <option value="6" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
-            <option value="5">BLAST XML</option>
-            <option value="0">Pairwise text</option>
-            <option value="0 -html">Pairwise HTML</option>
-            <option value="2">Query-anchored text</option>
-            <option value="2 -html">Query-anchored HTML</option>
-            <option value="4">Flat query-anchored text</option>
-            <option value="4 -html">Flat query-anchored HTML</option>
-            <!--
-            <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
-            -->
-        </param>
-        <conditional name="adv_opts">
-            <param name="adv_opts_selector" type="select" label="Advanced Options">
-              <option value="basic" selected="True">Hide Advanced Options</option>
-              <option value="advanced">Show Advanced Options</option>
-            </param>
-            <when value="basic" />
-            <when value="advanced">
-                <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
-                <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
-                <param name="matrix" type="select" label="Scoring matrix">
-                    <option value="BLOSUM90">BLOSUM90</option>
-                    <option value="BLOSUM80">BLOSUM80</option>
-                    <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
-                    <option value="BLOSUM50">BLOSUM50</option> 
-                    <option value="BLOSUM45">BLOSUM45</option>
-                    <option value="PAM250">PAM250</option>
-                    <option value="PAM70">PAM70</option>
-                    <option value="PAM30">PAM30</option>
-                </param>
-                <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
-                <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
-                    <validator type="in_range" min="0" />
-                </param>
-                <!-- I'd like word_size to be optional, with minimum 2 for blastp -->
-                <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
-                    <validator type="in_range" min="0" />
-                </param>
-                <!--
-                Can't use '-ungapped' on its own, error back is:
-                Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search
-                Tried using '-ungapped -comp_based_stats F' and tblastn crashed with 'Attempt to access NULL pointer.'
-                <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
-                -->
-                <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}">
-            <change_format>
-                <when input="out_format" value="0" format="txt"/>
-                <when input="out_format" value="0 -html" format="html"/>
-                <when input="out_format" value="2" format="txt"/>
-                <when input="out_format" value="2 -html" format="html"/>
-                <when input="out_format" value="4" format="txt"/>
-                <when input="out_format" value="4 -html" format="html"/>
-                <when input="out_format" value="5" format="blastxml"/>
-            </change_format>
-        </data>
-    </outputs>
-    <requirements>
-        <requirement type="binary">tblastn</requirement>
-    </requirements>
-    <tests>
-        <test>
-            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-10" />
-            <param name="out_format" value="5" />
-            <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="false" />
-            <param name="matrix" value="BLOSUM80" />
-            <param name="max_hits" value="0" />
-            <param name="word_size" value="0" />
-            <param name="parse_deflines" value="false" />
-            <output name="output1" file="tblastn_four_human_vs_rhodopsin.xml" ftype="blastxml" />
-        </test>
-        <test>
-            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-10" />
-            <param name="out_format" value="ext" />
-            <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="false" />
-            <param name="matrix" value="BLOSUM80" />
-            <param name="max_hits" value="0" />
-            <param name="word_size" value="0" />
-            <param name="parse_deflines" value="false" />
-            <output name="output1" file="tblastn_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-10" />
-            <param name="out_format" value="6" />
-            <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="false" />
-            <param name="matrix" value="BLOSUM80" />
-            <param name="max_hits" value="0" />
-            <param name="word_size" value="0" />
-            <param name="parse_deflines" value="false" />
-            <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <!-- Same as above, but parse deflines - on BLAST 2.2.25+ makes no difference -->
-            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-10" />
-            <param name="out_format" value="6" />
-            <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="false" />
-            <param name="matrix" value="BLOSUM80" />
-            <param name="max_hits" value="0" />
-            <param name="word_size" value="0" />
-            <param name="parse_deflines" value="true" />
-            <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="db_opts_selector" value="file" />
-            <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
-            <param name="database" value="" />
-            <param name="evalue_cutoff" value="1e-10" />
-            <param name="out_format" value="0 -html" />
-            <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="false" />
-            <param name="matrix" value="BLOSUM80" />
-            <param name="max_hits" value="0" />
-            <param name="word_size" value="0" />
-            <param name="parse_deflines" value="false" />
-            <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" />
-        </test>
-    </tests>
-    <help>
-    
-.. class:: warningmark
-
-**Note**. Database searches may take a substantial amount of time.
-For large input datasets it is advisable to allow overnight processing.  
-
------
-
-**What it does**
-
-Search a *translated nucleotide database* using a *protein query*,
-using the NCBI BLAST+ tblastn command line tool.
-
------
-
-**Output format**
-
-Because Galaxy focuses on processing tabular data, the default output of this
-tool is tabular. The standard BLAST+ tabular output contains 12 columns:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
-     1 qseqid    Query Seq-id (ID of your sequence)
-     2 sseqid    Subject Seq-id (ID of the database hit)
-     3 pident    Percentage of identical matches
-     4 length    Alignment length
-     5 mismatch  Number of mismatches
-     6 gapopen   Number of gap openings
-     7 qstart    Start of alignment in query
-     8 qend      End of alignment in query
-     9 sstart    Start of alignment in subject (database hit)
-    10 send      End of alignment in subject (database hit)
-    11 evalue    Expectation value (E-value)
-    12 bitscore  Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name     Description
------- ------------- -------------------------------------------
-    13 sallseqid     All subject Seq-id(s), separated by a ';'
-    14 score         Raw score
-    15 nident        Number of identical matches
-    16 positive      Number of positive-scoring matches
-    17 gaps          Total number of gaps
-    18 ppos          Percentage of positive-scoring matches
-    19 qframe        Query frame
-    20 sframe        Subject frame
-    21 qseq          Aligned part of query sequence
-    22 sseq          Aligned part of subject sequence
-    23 qlen          Query sequence length
-    24 slen          Subject sequence length
-====== ============= ===========================================
-
-The third option is BLAST XML output, which is designed to be parsed by
-another program, and is understood by some Galaxy tools.
-
-You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
-The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
-The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
-The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
-and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
-
--------
-
-**References**
-
-Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
-
-    </help>
-</tool>
diff --git a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
deleted file mode 100644
index bb96f972a9c..00000000000
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
+++ /dev/null
@@ -1,208 +0,0 @@
-<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.11">
-    <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description>
-    <!-- If job splitting is enabled, break up the query file into four -->
-    <parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism>
-    <version_command>tblastx -version</version_command>
-    <command interpreter="python">hide_stderr.py
-## The command is a Cheetah template which allows some Python based syntax.
-## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
-tblastx
--query "$query"
-#if $db_opts.db_opts_selector == "db":
-  -db "${db_opts.database.fields.path}"
-#else:
-  -subject "$db_opts.subject"
-#end if
--evalue $evalue_cutoff
--out $output1
-##Set the extended list here so if/when we add things, saved workflows are not affected
-#if str($out_format)=="ext":
-    -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
-#else:
-    -outfmt $out_format
-#end if
--num_threads 8
-#if $adv_opts.adv_opts_selector=="advanced":
-$adv_opts.filter_query
-$adv_opts.strand
--matrix $adv_opts.matrix
-## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
-## Note -max_target_seqs overrides -num_descriptions and -num_alignments
-#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
--max_target_seqs $adv_opts.max_hits
-#end if
-#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
--word_size $adv_opts.word_size
-#end if
-$adv_opts.parse_deflines
-## End of advanced options:
-#end if
-    </command>
-    <inputs>
-        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
-        <conditional name="db_opts">
-            <param name="db_opts_selector" type="select" label="Subject database/sequences">
-              <option value="db" selected="True">BLAST Database</option>
-              <option value="file">FASTA file</option>
-            </param>
-            <when value="db">
-                <param name="database" type="select" label="Nucleotide BLAST database">
-                    <options from_file="blastdb.loc">
-                      <column name="value" index="0"/>
-                      <column name="name" index="1"/>
-                      <column name="path" index="2"/>
-                    </options>
-                </param>
-                <param name="subject" type="hidden" value="" /> 
-            </when>
-            <when value="file">
-                <param name="database" type="hidden" value="" /> 
-                <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> 
-            </when>
-        </conditional>
-        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
-        <param name="out_format" type="select" label="Output format">
-            <option value="6" selected="True">Tabular (standard 12 columns)</option>
-            <option value="ext">Tabular (extended 24 columns)</option>
-            <option value="5">BLAST XML</option>
-            <option value="0">Pairwise text</option>
-            <option value="0 -html">Pairwise HTML</option>
-            <option value="2">Query-anchored text</option>
-            <option value="2 -html">Query-anchored HTML</option>
-            <option value="4">Flat query-anchored text</option>
-            <option value="4 -html">Flat query-anchored HTML</option>
-            <!--
-            <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
-            -->
-        </param>
-        <conditional name="adv_opts">
-            <param name="adv_opts_selector" type="select" label="Advanced Options">
-              <option value="basic" selected="True">Hide Advanced Options</option>
-              <option value="advanced">Show Advanced Options</option>
-            </param>
-            <when value="basic" />
-            <when value="advanced">
-                <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
-                <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
-                <param name="strand" type="select" label="Query strand(s) to search against database/subject">
-                    <option value="-strand both">Both</option>
-                    <option value="-strand plus">Plus (forward)</option>
-                    <option value="-strand minus">Minus (reverse complement)</option>
-                </param>
-                <param name="matrix" type="select" label="Scoring matrix">
-                    <option value="BLOSUM90">BLOSUM90</option>
-                    <option value="BLOSUM80">BLOSUM80</option>
-                    <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
-                    <option value="BLOSUM50">BLOSUM50</option> 
-                    <option value="BLOSUM45">BLOSUM45</option>
-                    <option value="PAM250">PAM250</option>
-                    <option value="PAM70">PAM70</option>
-                    <option value="PAM30">PAM30</option>
-                </param>
-                <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
-                <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
-                    <validator type="in_range" min="0" />
-                </param>
-                <!-- I'd like word_size to be optional, with minimum 2 for tblastx -->
-                <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
-                    <validator type="in_range" min="0" />
-                </param>
-                <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="output1" format="tabular" label="tblastx on ${db_opts.db_opts_selector}">
-            <change_format>
-                <when input="out_format" value="0" format="txt"/>
-                <when input="out_format" value="0 -html" format="html"/>
-                <when input="out_format" value="2" format="txt"/>
-                <when input="out_format" value="2 -html" format="html"/>
-                <when input="out_format" value="4" format="txt"/>
-                <when input="out_format" value="4 -html" format="html"/>
-                <when input="out_format" value="5" format="blastxml"/>
-            </change_format>
-        </data>
-    </outputs>
-    <requirements>
-        <requirement type="binary">tblastx</requirement>
-    </requirements>
-    <help>
-    
-.. class:: warningmark
-
-**Note**. Database searches may take a substantial amount of time.
-For large input datasets it is advisable to allow overnight processing.  
-
------
-
-**What it does**
-
-Search a *translated nucleotide database* using a *protein query*,
-using the NCBI BLAST+ tblastx command line tool.
-
------
-
-**Output format**
-
-Because Galaxy focuses on processing tabular data, the default output of this
-tool is tabular. The standard BLAST+ tabular output contains 12 columns:
-
-====== ========= ============================================
-Column NCBI name Description
------- --------- --------------------------------------------
-     1 qseqid    Query Seq-id (ID of your sequence)
-     2 sseqid    Subject Seq-id (ID of the database hit)
-     3 pident    Percentage of identical matches
-     4 length    Alignment length
-     5 mismatch  Number of mismatches
-     6 gapopen   Number of gap openings
-     7 qstart    Start of alignment in query
-     8 qend      End of alignment in query
-     9 sstart    Start of alignment in subject (database hit)
-    10 send      End of alignment in subject (database hit)
-    11 evalue    Expectation value (E-value)
-    12 bitscore  Bit score
-====== ========= ============================================
-
-The BLAST+ tools can optionally output additional columns of information,
-but this takes longer to calculate. Most (but not all) of these columns are
-included by selecting the extended tabular output. The extra columns are
-included *after* the standard 12 columns. This is so that you can write
-workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
-
-====== ============= ===========================================
-Column NCBI name     Description
------- ------------- -------------------------------------------
-    13 sallseqid     All subject Seq-id(s), separated by a ';'
-    14 score         Raw score
-    15 nident        Number of identical matches
-    16 positive      Number of positive-scoring matches
-    17 gaps          Total number of gaps
-    18 ppos          Percentage of positive-scoring matches
-    19 qframe        Query frame
-    20 sframe        Subject frame
-    21 qseq          Aligned part of query sequence
-    22 sseq          Aligned part of subject sequence
-    23 qlen          Query sequence length
-    24 slen          Subject sequence length
-====== ============= ===========================================
-
-The third option is BLAST XML output, which is designed to be parsed by
-another program, and is understood by some Galaxy tools.
-
-You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
-The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
-The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
-The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
-and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
-
--------
-
-**References**
-
-Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
-
-    </help>
-</tool>