diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 47cf0c1e734..e05bdfdfe6a 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -155,6 +155,7 @@
     <tool file="taxonomy/t2t_report.xml" />
     <tool file="taxonomy/t2ps_wrapper.xml" />
     <tool file="taxonomy/find_diag_hits.xml" />
+    <tool file="taxonomy/lca.xml" />
     <tool file="taxonomy/poisson2test.xml" />
   </section>
   <section name="Solexa tools" id="solexa_tools">
diff --git a/tools/taxonomy/lca.py b/tools/taxonomy/lca.py
index 0b9785d9dd5..d70425db366 100644
--- a/tools/taxonomy/lca.py
+++ b/tools/taxonomy/lca.py
@@ -1,10 +1,9 @@
 #!/usr/bin/env python
 #Guruprasad Ananda
 """
-This tool provides the SQL "group by" functionality.
+Least Common Ancestor tool.
 """
 import sys, string, re, commands, tempfile, random
-#from rpy import *
 
 def stop_err(msg):
     sys.stderr.write(msg)
@@ -42,8 +41,8 @@ def main():
         """
     except:
         stop_err("Syntax error: Use correct syntax: program infile outfile")
+    
     group_col = 0
-
     tmpfile = tempfile.NamedTemporaryFile()
 
     try:
@@ -68,10 +67,6 @@ def main():
     prev_vals = []
     remaining_vals = []
     skipped_lines = 0
-    first_invalid_line = 0
-    invalid_line = ''
-    invalid_value = ''
-    invalid_column = 0
     fout = open(outfile, "w")
     cols = range(1,25)
     block_valid = False
@@ -104,9 +99,10 @@ def main():
                         out_list[0] = str(prev_item)
                         out_list[1] = str(prev_vals[0][0])
                         out_list[2] = str(prev_vals[1][0])
-                        out_list[24] = str(prev_vals[23][0])
-                        #print >> fout, prev_vals
-                        #sys.exit()
+                        try:
+                            out_list[24] = str(prev_vals[23][0])
+                        except:
+                            pass
                         for k, col in enumerate(cols):
                             if col >= 3 and col < 24:
                                 if len(set(prev_vals[k])) == 1:
@@ -116,17 +112,14 @@ def main():
                         while k < 23:
                             out_list[k+1] = 'n' 
                             k += 1
-                            
-                        # print >>fout, '\t'.join(out_list)
                         
                         if rank_bound == 0:     
-                            print >>fout, ''.join(out_list)
-                            print 'n'*( 24 - rank_bound )
+                            print >>fout, '\t'.join(out_list).strip()
+                            #print 'n'*( 24 - rank_bound )
                         else:
-                            print '\t'.join(out_list[rank_bound:24])
+                            #print '\t'.join(out_list[rank_bound:24])
                             if ''.join(out_list[rank_bound:24]) != 'n'*( 24 - rank_bound ):
-                                print >>fout, '\t'.join(out_list)
-
+                                print >>fout, '\t'.join(out_list).strip()
                         
                         block_valid = True
                         prev_item = item   
@@ -145,21 +138,21 @@ def main():
                         val_list.append(fields[col].strip())
                         prev_vals.append(val_list)
             
-            except Exception, exc:
+            except:
                 skipped_lines += 1
-                if not first_invalid_line:
-                    first_invalid_line = ii+1
         else:
             skipped_lines += 1
-            if not first_invalid_line:
-                first_invalid_line = ii+1
-     
+            
     # Handle the last grouped value
     out_list = ['']*25
     out_list[0] = str(prev_item)
     out_list[1] = str(prev_vals[0][0])
     out_list[2] = str(prev_vals[1][0])
-    out_list[24] = str(prev_vals[23][0])
+    try:
+        out_list[24] = str(prev_vals[23][0])
+    except:
+        pass
+
     for k, col in enumerate(cols):
         if col >= 3 and col < 24:
             if len(set(prev_vals[k])) == 1:
@@ -171,16 +164,15 @@ def main():
         k += 1
     
     if rank_bound == 0:     
-        print >>fout, '\t'.join(out_list)
+        print >>fout, '\t'.join(out_list).strip()
     else:
-        print ''.join(out_list[rank_bound:24])
-        print 'n'*( 24 - rank_bound )
+        #print ''.join(out_list[rank_bound:24])
+        #print 'n'*( 24 - rank_bound )
         if ''.join(out_list[rank_bound:24]) != 'n'*( 24 - rank_bound ):
-            print >>fout, '\t'.join(out_list)
+            print >>fout, '\t'.join(out_list).strip()
         
     if skipped_lines > 0:
-        msg= "Skipped %d invalid lines starting with line %d.  Value '%s' in column %d is not numeric." % ( skipped_lines, first_invalid_line, invalid_value, invalid_column )
-        print msg
+        print "Skipped %d invalid lines." % ( skipped_lines )
     
 if __name__ == "__main__":
     main()
\ No newline at end of file
diff --git a/tools/taxonomy/lca.xml b/tools/taxonomy/lca.xml
index f608a16cfc3..ca5e246d41a 100644
--- a/tools/taxonomy/lca.xml
+++ b/tools/taxonomy/lca.xml
@@ -1,12 +1,12 @@
-<tool id="lca1" name="Least Common Ancestor" version="1.0.0">
+<tool id="lca1" name="Find lowest diagnostic rank" version="1.0.0">
   <description></description>
   <command interpreter="python">
     lca.py $input1 $out_file1 $rank_bound
   </command>
   <inputs>
-    <param format="taxonomy" name="input1" type="data" label="Select taxonomy dataset"/>
-    <param name="rank_bound" label="rank bound" type="select" help="Choose smallest diagnostic level">
-        <option value="0">Everything</option>
+    <param format="taxonomy" name="input1" type="data" label="for taxonomy dataset"/>
+    <param name="rank_bound" label="require the lowest rank to be at least" type="select">
+        <option value="0">No restriction</option>
         <option value="3">Superkingdom</option>
         <option value="4">Kingdom</option>
         <option value="5">Subkingdom</option>
@@ -32,13 +32,54 @@
   </inputs>
   <outputs>
     <data format="taxonomy" name="out_file1" metadata_source="input1" />
-  </outputs>
+  </outputs>
+  <tests>
+ <test>
+      <param name="input1" value="lca_input.taxonomy" ftype="taxonomy"/>
+      <param name="rank_bound" value="0" />
+      <output name="out_file1" file="lca_output.taxonomy" ftype="taxonomy"/>
+ </test> 
+ </tests>
 
-<help>
+ <help>
 
 **What it does**
 
-When performing metagenomic analyses it is often necessary to identify sequence reads corresponding to a particular taxonomic group, or, in other words, diagnostic of a particular taxonomic rank. This utility performs this analysis. It takes data generated by *Taxonomy manipulation->Fetch Taxonomic Ranks* as input and outputs either a list of sequence reads unique to a particular taxonomic rank, or a list of taxonomic ranks and the count of unique reads corresponding to each rank. 
+This tool identifies the lowest taxonomic rank for which a mategenomic sequencing read is diagnostic. It takes datasets produced by *Fetch Taxonomic Ranks* tool (aka Taxonomy format) as the input. 
+
+-------
+
+**Example**
+
+Suppose you have two reads, **read_1** and **read_2**, with the following taxonomic profiles (scroll sideways to see the entire dataset)::
+  
+    read_1 1 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus1 subgenus1 species1 subspecies1
+    read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus2 subgenus2 species2 subspecies2
+    read_2 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum3 subphylum3 superclass3 class3 subclass3 superorder3 order3 suborder3 superfamily3 family3 subfamily3 tribe3 subtribe3 genus3 subgenus3 species3 subspecies3
+    read_2 4 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum4 subphylum4 superclass4 class4 subclass4 superorder4 order4 suborder4 superfamily4 family4 subfamily4 tribe4 subtribe4 genus4 subgenus4 species4 subspecies4
+
+For **read_1** taxonomic labels are consistent until the genus level, where the taxonomy splits into two branches, one ending with *subspecies1* and the other with *subspecies2*. This implies **that the lowest taxomomic rank read_1 can identify is SUBTRIBE**.  Similarly, read_2 is diagnostic up until the **superphylum** level.  As a results the output of this tool will be::
+
+    read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 n n n n
+    read_2 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 n       n          n           n      n         n           n      n         n            n       n          n      n         n n n n
+    
+where, **n** means *EMPTY*. 
+
+--------
+
+**What's up with the drop down?**
+
+Why do we need the *require the lowest rank to be at least* dropdown?  Let's look at the above example again. Suppose you need to find only those reads that are diagnostic on at least phylum level. To do this you need to set the *require the lowest rank to be at least* to **phylum**. As a result your output will look like this::
+
+    read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 n n n n
+
+.. class:: infomark
+    
+Note, that **read_2** is now omitted as it matches two phyla (**phylum3** and **phylum4**) and therefore is not diagnostic (but rather cosmopolitan) on *phylum* level. 
+
+
+
+
 
 </help>
 </tool>
\ No newline at end of file