diff --git a/tools/extract/genebed_maf_to_fasta_code.py b/tools/extract/genebed_maf_to_fasta_code.py
index 211fef66f09..308204aa883 100644
--- a/tools/extract/genebed_maf_to_fasta_code.py
+++ b/tools/extract/genebed_maf_to_fasta_code.py
@@ -50,37 +50,7 @@ def get_available_species( maf_source_type ):
         return available_sets
     else:
         try:
-            rval = []
-            species={}
-            input_filename = maf_source_type['input2'].file_name
-            try:
-                file_in = open(input_filename, 'r')
-                maf_reader = bx.align.maf.Reader( file_in )
-                
-                for i, m in enumerate( maf_reader ):
-                    l = m.components
-                    for c in l:
-                        spec,chrom = bx.align.maf.src_split( c.src )
-                        if not spec or not chrom:
-                            spec = chrom = c.src
-                        if spec not in species:
-                            species[spec]={"bases":0,"nongaps":0}
-                        species[spec]["bases"] = species[spec]["bases"] + c.size + c.text.count("-")
-                        species[spec]["nongaps"] = species[spec]["nongaps"] + c.size 
-                
-                file_in.close()
-            except Exception:
-                return [("There is a problem with your MAF file",'None',True)]
-            species_names = species.keys()
-            species_names.sort()
-            
-            for spec in species_names:
-                #species_sequence[spec] = "".join(species_sequence[spec])
-                
-                display = "%s: %i nongap, %i total bases" % (spec, species[spec]["nongaps"], species[spec]["bases"] )
-                rval.append( ( display,spec,True) )
-                    
-            return rval
+            return map(lambda spec: (spec, spec, True), maf_source_type['input2'].metadata.species)
         except:
             return [("<B>You must wait for the MAF file to be created before you can use this tool.</B>",'None',True)]
 
diff --git a/tools/extract/interval2maf.xml b/tools/extract/interval2maf.xml
index b91ae98f81a..2db4fcece5f 100644
--- a/tools/extract/interval2maf.xml
+++ b/tools/extract/interval2maf.xml
@@ -24,7 +24,7 @@
     </page>
    </inputs>
   <outputs>
-    <data format="maf" name="out_file1" metadata_source="input1"/>
+    <data format="maf" name="out_file1"/>
   </outputs>
   <tests>
     <test>
diff --git a/tools/extract/interval_maf_to_merged_fasta_code.py b/tools/extract/interval_maf_to_merged_fasta_code.py
index 00483c7e0d8..e28c7acebc3 100644
--- a/tools/extract/interval_maf_to_merged_fasta_code.py
+++ b/tools/extract/interval_maf_to_merged_fasta_code.py
@@ -49,37 +49,7 @@ def get_available_species( maf_source_type ):
         return available_sets
     else:
         try:
-            rval = []
-            species={}
-            input_filename = maf_source_type['input2'].file_name
-            try:
-                file_in = open(input_filename, 'r')
-                maf_reader = bx.align.maf.Reader( file_in )
-                
-                for i, m in enumerate( maf_reader ):
-                    l = m.components
-                    for c in l:
-                        spec,chrom = bx.align.maf.src_split( c.src )
-                        if not spec or not chrom:
-                            spec = chrom = c.src
-                        if spec not in species:
-                            species[spec]={"bases":0,"nongaps":0}
-                        species[spec]["bases"] = species[spec]["bases"] + c.size + c.text.count("-")
-                        species[spec]["nongaps"] = species[spec]["nongaps"] + c.size 
-                
-                file_in.close()
-            except Exception:
-                return [("There is a problem with your MAF file",'None',True)]
-            species_names = species.keys()
-            species_names.sort()
-            
-            for spec in species_names:
-                #species_sequence[spec] = "".join(species_sequence[spec])
-                
-                display = "%s: %i nongap, %i total bases" % (spec, species[spec]["nongaps"], species[spec]["bases"] )
-                rval.append( ( display,spec,True) )
-                    
-            return rval
+            return map(lambda spec: (spec, spec, True), maf_source_type['input2'].metadata.species)
         except:
             return [("<B>You must wait for the MAF file to be created before you can use this tool.</B>",'None',True)]
 
diff --git a/tools/filters/maf/maf_by_block_number.xml b/tools/filters/maf/maf_by_block_number.xml
index b702f16731b..a1d6e06cc39 100644
--- a/tools/filters/maf/maf_by_block_number.xml
+++ b/tools/filters/maf/maf_by_block_number.xml
@@ -4,13 +4,16 @@
   <inputs>
     <page>
         <param format="text" name="input1" type="data" label="Block Numbers"/>
-        <param name="block_col" type="integer" label="Column containing Block number" value="1" help="Use 1 if your file contains only block numbers"/>
         <param format="maf" name="input2" label="MAF File" type="data"/>
     </page>
+    <page>
+        <param name="block_col" type="select" label="Column containing Block number" dynamic_options="get_columns(input1)"/>
+    </page>
    </inputs>
   <outputs>
     <data format="maf" name="out_file1" />
   </outputs>
+  <code file="maf_by_block_number_code.py"/>
   <tests>
     <test>
       <param name="input1" value="maf_by_block_numbers.dat"/>
diff --git a/tools/filters/maf/maf_by_block_number_code.py b/tools/filters/maf/maf_by_block_number_code.py
new file mode 100644
index 00000000000..38cc90c7277
--- /dev/null
+++ b/tools/filters/maf/maf_by_block_number_code.py
@@ -0,0 +1,9 @@
+#!/usr/bin/env python2.4
+#Dan Blankenberg
+"""
+Returns valid column numbers, defaulting to 1 for text files
+"""
+
+def get_columns(dataset):
+    if not dataset.metadata.columns: return [("1", "1", True)]
+    return map(lambda col: (str(col), str(col), False), range(1, dataset.metadata.columns+1))
diff --git a/tools/filters/maf/maf_limit_to_species.xml b/tools/filters/maf/maf_limit_to_species.xml
index 786123cfdb0..e8e308a0062 100644
--- a/tools/filters/maf/maf_limit_to_species.xml
+++ b/tools/filters/maf/maf_limit_to_species.xml
@@ -16,7 +16,7 @@
             </param>
         </page>
         <page>
-            <param name="species" type="select" label="Species to keep" dynamic_options="get_available_species( input1.file_name )" display="checkboxes" multiple="true"/>
+            <param name="species" type="select" label="Species to keep" dynamic_options="map(lambda spec: (spec, spec, True), input1.metadata.species)" display="checkboxes" multiple="true"/>
         </page>
     </inputs>
     <outputs>
@@ -42,6 +42,6 @@ This tool allows the user to remove any undesired species from a MAF file. Colum
  * **Exclude blocks with have only one species** - if this option is set to **YES** all single sequence alignment blocks WILL NOT be returned.
 
     </help>
-    <code file="maf_limit_to_species_code.py"/>
+    <!--<code file="maf_limit_to_species_code.py"/>-->
 </tool>
 
diff --git a/tools/filters/maf/maf_stats.py b/tools/filters/maf/maf_stats.py
index 89d8e309ebe..4c4f6eca7d3 100644
--- a/tools/filters/maf/maf_stats.py
+++ b/tools/filters/maf/maf_stats.py
@@ -22,6 +22,9 @@ def __main__():
     chr_col  = int(sys.argv[5].strip())-1
     start_col = int(sys.argv[6].strip())-1
     end_col = int(sys.argv[7].strip())-1
+    summary = sys.argv[8].strip()
+    if summary.lower() == "true": summary = True
+    else: summary = False
     
     index = None
     index_filename = None
@@ -79,7 +82,7 @@ def __main__():
                     continue
             index = bx.align.maf.MultiIndexed( maf_sets[input_maf_filename]['paths'], keep_open=True, parse_e_rows=True )
         except Exception, exc:
-            print >>sys.stdout, 'interval2maf.py initialization error -> %s' % exc 
+            print >>sys.stdout, 'maf_stats.py initialization error -> %s' % exc 
             sys.exit()
     else:
         print >>sys.stdout, 'Invalid source type specified: %s' % maf_source_type 
@@ -88,6 +91,8 @@ def __main__():
     out = open(output_filename, 'w')
     
     num_region = 0
+    species_summary = {}
+    total_length = 0
     #loop through interval file
     for region in bx.intervals.io.NiceReaderWrapper( open(input_interval_filename, 'r' ), chrom_col=chr_col, start_col=start_col, end_col=end_col, fix_strand=True, return_header=False, return_comments=False):
         sequences = {dbkey: [ False for i in range( region.end - region.start)]}
@@ -96,6 +101,8 @@ def __main__():
         start = region.start
         end = region.end
         
+        total_length += (end - start)
+        
         blocks = index.get( src, start, end )
         for maf in blocks:
             #make sure all species are known
@@ -135,15 +142,25 @@ def __main__():
                     if i in gaps: gap_offset += 1
                     elif c.text[i] not in ['-']: sequences[spec][i-gap_offset+slice_start-start] = True
             
-        #print sequences
-        out.write("%s\t%s\t%s\t%s\n" % ( "\t".join(region.fields), dbkey, sequences[dbkey].count(True), sequences[dbkey].count(False) ) )
-        keys = sequences.keys()
-        keys.remove(dbkey)
-        keys.sort()
-        for key in keys:
-            out.write("%s\t%s\t%s\t%s\n" % ( "\t".join(region.fields), key, sequences[key].count(True), sequences[key].count(False) ) )
+        if summary:
+            #record summary
+            for key in sequences.keys():
+                if key not in species_summary: species_summary[key] = 0
+                species_summary[key] = species_summary[key] + sequences[key].count(True)
+        else:
+            #print sequences
+            out.write("%s\t%s\t%s\t%s\n" % ( "\t".join(region.fields), dbkey, sequences[dbkey].count(True), sequences[dbkey].count(False) ) )
+            keys = sequences.keys()
+            keys.remove(dbkey)
+            keys.sort()
+            for key in keys:
+                out.write("%s\t%s\t%s\t%s\n" % ( "\t".join(region.fields), key, sequences[key].count(True), sequences[key].count(False) ) )
         num_region += 1
-    print "%i regions were processed." % num_region
+    if summary:
+        out.write("#species\tnucleotides\tcoverage\n")
+        for spec in species_summary:
+            out.write("%s\t%s\t%.4f\n" % ( spec, species_summary[spec], float(species_summary[spec]) / total_length ))
+    print "%i regions were processed with a total length of %i." % (num_region, total_length)
     out.close()
     if index_filename is not None:
         os.unlink(index_filename)
diff --git a/tools/filters/maf/maf_stats.xml b/tools/filters/maf/maf_stats.xml
index fe2af56f9ae..16bebf18856 100644
--- a/tools/filters/maf/maf_stats.xml
+++ b/tools/filters/maf/maf_stats.xml
@@ -3,9 +3,9 @@
   <command interpreter="python2.4">
 maf_stats.py
 #if $maf_source_type.maf_source == "user":
-$maf_source_type.maf_source $input2 $input1 $out_file1 $dbkey $input1_chromCol $input1_startCol $input1_endCol
+$maf_source_type.maf_source $input2 $input1 $out_file1 $dbkey $input1_chromCol $input1_startCol $input1_endCol $summary
 #else:
-$maf_source_type.maf_source $maf_source_type.mafType $input1 $out_file1 $dbkey $input1_chromCol $input1_startCol $input1_endCol
+$maf_source_type.maf_source $maf_source_type.mafType $input1 $out_file1 $dbkey $input1_chromCol $input1_startCol $input1_endCol $summary
 #end if
   </command>
   <inputs>
@@ -25,6 +25,10 @@ $maf_source_type.maf_source $maf_source_type.mafType $input1 $out_file1 $dbkey $
                 <param name="mafType" label="MAF Type" type="select" dynamic_options="get_available_data( input1.dbkey )"/>
             </when>
         </conditional>
+        <param name="summary" type="select" label="Type of Output">
+          <option value="false" selected="true">Coverage by Region</option>
+          <option value="true">Summarize Coverage</option>
+        </param>
     </page>
    </inputs>
   <outputs>
@@ -36,6 +40,7 @@ $maf_source_type.maf_source $maf_source_type.mafType $input1 $out_file1 $dbkey $
       <param name="maf_source" value="cached"/>
       <param name="mafType" value="8_WAY_MULTIZ_hg17"/>
       <output name="out_file1" file="maf_stats_interval_out.dat"/>
+      <param name="summary" value="false"/>
     </test>
   </tests>
   <help>
@@ -61,7 +66,19 @@ Consider the interval: "chrX 1000 1100 myInterval"
     
     YYY = number of gaps
 
+----
 
+Alternatively, you can request only summary information for a set of intervals:
+  
+  ========  ===========  ========
+  #species  nucleotides  coverage
+  ========  ===========  ========
+  hg18         30639      0.2372
+  rheMac2      7524       0.0582
+  panTro2      30390      0.2353
+  ========  ===========  ========
+
+  where **coverage** is the number of nucleotides divided by the total length of the provided intervals.
   </help>
   <code file="maf_stats_code.py"/>
 </tool>
diff --git a/tools/filters/maf/maf_stats_code.py b/tools/filters/maf/maf_stats_code.py
index 43501f76a76..a991d10b7a6 100644
--- a/tools/filters/maf/maf_stats_code.py
+++ b/tools/filters/maf/maf_stats_code.py
@@ -45,3 +45,6 @@ def exec_before_job(app, inp_data, out_data, param_dict, tool):
                 data.name = data.name + " [" + maf_sets[str(param_dict['maf_source_type']['mafType'])]['description'] + "]"
             except KeyError:
                 data.name = data.name + " [unknown MAF source specified]"
+    if param_dict['summary'].lower() == "true":
+        for name, data in out_data.items():
+            data.change_datatype('tabular')
diff --git a/tools/filters/maf/maf_thread_for_species.xml b/tools/filters/maf/maf_thread_for_species.xml
index bb43d2eed33..77bd998a4f6 100644
--- a/tools/filters/maf/maf_thread_for_species.xml
+++ b/tools/filters/maf/maf_thread_for_species.xml
@@ -6,7 +6,7 @@
             <param format="maf" name="input1" type="data" label="MAF file"/>
         </page>
         <page>
-            <param name="species" type="select" label="Species to keep" dynamic_options="get_available_species( input1.file_name )" display="checkboxes" multiple="true"/>
+            <param name="species" type="select" label="Species to keep" dynamic_options="map(lambda spec: (spec, spec, True), input1.metadata.species)" display="checkboxes" multiple="true"/>
         </page>
     </inputs>
     <outputs>
@@ -51,6 +51,6 @@ results in::
 
 
     </help>
-    <code file="maf_thread_for_species_code.py"/>
+    <!--<code file="maf_thread_for_species_code.py"/>-->
 </tool>
 
diff --git a/tools/filters/maf/maf_to_bed.xml b/tools/filters/maf/maf_to_bed.xml
index 669c2851d3a..4456395db63 100644
--- a/tools/filters/maf/maf_to_bed.xml
+++ b/tools/filters/maf/maf_to_bed.xml
@@ -6,7 +6,7 @@
             <param format="maf" name="input1" type="data" label="MAF file to convert"/>
         </page>
         <page>
-            <param name="species" type="select" label="Select species" dynamic_options="get_available_species( input1.dbkey, input1.file_name )" display="checkboxes" multiple="true" help="a separate history item will be created for each checked species" />
+            <param name="species" type="select" label="Select species" dynamic_options="map(lambda spec: (spec, spec, True), input1.metadata.species)" display="checkboxes" multiple="true" help="a separate history item will be created for each checked species" />
             <param name="complete_blocks" type="select">
               <label>Exclude blocks which have a requested species missing</label>
               <option value="partial_allowed">include blocks with missing species</option>
diff --git a/tools/filters/maf/maf_to_fasta.xml b/tools/filters/maf/maf_to_fasta.xml
index c35e4d95fe4..c073f263880 100644
--- a/tools/filters/maf/maf_to_fasta.xml
+++ b/tools/filters/maf/maf_to_fasta.xml
@@ -15,7 +15,7 @@
               <option value="concatenated">One Sequence per Species</option>
             </param>
             <when value="multiple">
-	          <param name="species" type="select" label="Select species" dynamic_options="get_available_species( input1.file_name )" display="checkboxes" multiple="true" help="checked taxa will be included in the output"/>
+	          <param name="species" type="select" label="Select species" dynamic_options="map(lambda spec: (spec, spec, True), input1.metadata.species)" display="checkboxes" multiple="true" help="checked taxa will be included in the output"/>
 	          <param name="complete_blocks" type="select">
 	            <label>Choose to</label>
 	            <option value="partial_allowed">include blocks with missing species</option>
@@ -23,7 +23,7 @@
 	          </param>
             </when>
             <when value="concatenated">
-                <param name="species" type="select" label="Species to extract" dynamic_options="get_available_species( input1.file_name )" display="checkboxes" multiple="true"/>
+                <param name="species" type="select" label="Species to extract" dynamic_options="map(lambda spec: (spec, spec, True), input1.metadata.species)" display="checkboxes" multiple="true"/>
             </when>
         </conditional>
       </page>
@@ -184,5 +184,5 @@ will be converted to (**note** that the second MAF block, which does not have mm
 
 
     </help>
-    <code file="maf_to_fasta_code.py"/>
+    <!--<code file="maf_to_fasta_code.py"/>-->
 </tool>