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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks commit 2c1d4da58bb81f0b7232a1b3f0b3a0fde752de33
author earlhaminst
date Thu, 12 Apr 2018 06:59:23 -0400
parents
children
files gblocks.xml test-data/Gblocks_Results_And_Parameters_on_data_95_html.html test-data/Gblocks_Selected_Blocks_on_data_95.txt test-data/Gblocks_on_data_95.txt test-data/nad3.fasta
diffstat 5 files changed, 424 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gblocks.xml	Thu Apr 12 06:59:23 2018 -0400
@@ -0,0 +1,123 @@
+<tool id="gblocks" name="Gblocks" version="0.91b">
+    <description>Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis</description>
+    <requirements>
+        <requirement type="package" version="0.91b">gblocks</requirement>
+    </requirements>
+    <command><![CDATA[
+ln -s '$inputFile' input.pir && Gblocks
+input.pir
+-t=$t
+#if $advanced.a == '-a'
+    #if str($advanced.b1)
+        -b1=$advanced.b1
+    #end if
+    #if str($advanced.b2)
+        -b2=$advanced.b2
+    #end if
+    -b3=$advanced.b3
+    -b4=$advanced.b4
+    -b5=$advanced.b5
+    -b6=$advanced.b6
+    -b0=$advanced.b0
+#end if
+#set $output_opt = ''
+#if $outputs
+    #set $outputs_arr = str($outputs).split(',')
+    #for $o in $outputs_arr
+        #set $output_opt += $o + '=y '
+    #end for
+#else
+    #set $outputs_arr = []
+#end if
+#if $output_opt
+    #set $output_opt = $output_opt[:-1]
+#end if
+$output_opt
+> '$outputFile'
+    ]]></command>
+    <inputs>
+        <param name="inputFile" type="data" format="fasta,pir" label="Multiple Sequence Alignment" help="Multiple Sequence Alignment in Fasta format." />
+        <param argument="-t" type="select" label="Type Of Sequence">
+            <option value="p" selected="true">Protein</option>
+            <option value="d">DNA</option>
+            <option value="c">Codons</option>
+        </param>
+        <conditional name="advanced">
+            <param name="a" type="select" label="Specify Advanced Parameters">
+                <option value="-a">Yes</option>
+                <option value="" selected="true">No</option>
+            </param>
+            <when value="" />
+            <when value="-a">
+                <param argument="-b1" type="integer" min="1" value="" optional="true" label="Minimum number of sequences for a conserved position" help="Any integer bigger than half the number of sequences and smaller or equal than the total number of sequences" />
+                <param argument="-b2" type="integer" min="1" value="" optional="true" label="Minimum number of sequences for a flank position" help="Any integer equal or bigger than minimum number of sequences for a conserved position" />
+                <param argument="-b3" type="integer" value="8" label="Maximum number of contiguous nonconserved positions" />
+                <param argument="-b4" type="integer" value="10" min="2" label="Minimum length of a block" />
+                <param argument="-b5" type="select" label="Allowed gap positions">
+                    <option value="n" selected="true">None</option>
+                    <option value="h">With Half</option>
+                    <option value="a">All</option>
+                </param>
+                <param argument="-b6" type="select" label="Use similarity matrices">
+                    <option value="y" selected="true">Yes</option>
+                    <option value="n">No</option>
+                </param>
+                <param argument="-b0" type="integer" value="10" min="2" label="Minimum length of an intial block" />
+            </when>
+        </conditional> 
+        <param name="outputs" type="select" multiple="true" optional="true" display="checkboxes" label="Output formats">
+            <option value="-s" selected="true">Selected blocks</option>
+            <option value="-p" selected="true">Results and parameters File</option>
+            <option value="-n">Nonconserved blocks</option>
+            <option value="-u">Ungapped alignment</option>
+            <option value="-k">Mask file with the selected blocks</option>
+            <option value="-d">Postscript file with the selected blocks</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="outputFile" format="txt" label="${tool.name} on ${on_string}" />
+        <data name="Results_and_parameters_file" format="html" from_work_dir="input.pir-gb.htm" label="${tool.name} Results and parameters on ${on_string}" >
+            <filter>outputs and '-p' in outputs</filter>
+        </data>
+        <data name="Selected_blocks" format="txt" from_work_dir="input.pir-gb" label="${tool.name} Selected blocks on ${on_string}" >
+            <filter>outputs and '-s' in outputs</filter>
+        </data>
+        <data name="Nonconserved_blocks" format="txt" from_work_dir="input.pir-gbComp" label="${tool.name} Nonconserved blocks on ${on_string}" >
+            <filter>outputs and '-n' in outputs</filter>
+        </data>
+        <data name="Ungapped_alignment" format="txt" from_work_dir="input.pir--" label="${tool.name} Ungapped alignment on ${on_string}" >
+            <filter>outputs and '-u' in outputs</filter>
+        </data>
+        <data name="Masked_file_with_the_selected_blocks" format="txt" from_work_dir="input.pir-gbMask" label="${tool.name} Masked file with the selected blocks on ${on_string}" >
+            <filter>outputs and '-k' in outputs</filter>
+        </data>
+        <data name="Postscript_file_with_the_selected_blocks" format="eps" from_work_dir="input.pir-gbPS" label="${tool.name} Postscript on ${on_string}" >
+            <filter>outputs and '-d' in outputs</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputFile" ftype="fasta" value="nad3.fasta" />
+            <param name="-t" value="p" />
+            <param name="outputs" value="-s,-p" />
+            <output name="outputFile" file="Gblocks_on_data_95.txt" />
+            <output name="Results_and_parameters_file" file="Gblocks_Results_And_Parameters_on_data_95_html.html" />
+            <output name="Selected_blocks" file="Gblocks_Selected_Blocks_on_data_95.txt" />
+        </test>
+        <test>
+            <param name="inputFile" ftype="fasta" value="nad3.fasta" />
+            <param name="-t" value="p" />
+            <param name="outputs" value="-s" />
+            <output name="outputFile" file="Gblocks_on_data_95.txt" />
+            <output name="Selected_blocks" file="Gblocks_Selected_Blocks_on_data_95.txt" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Simple wrapper for `Gblocks`_. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
+
+.. _Gblocks: http://molevol.cmima.csic.es/castresana/Gblocks.html
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/oxfordjournals.molbev.a026334</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Gblocks_Results_And_Parameters_on_data_95_html.html	Thu Apr 12 06:59:23 2018 -0400
@@ -0,0 +1,124 @@
+<html>
+<head>
+<meta http-equiv=content-type content=text/html;charset=ISO-8859-1>
+<title>input.pir</title>
+<style media=screen type=text/css><!--
+.BL {background-color:navy;color:navy}
+.A1 {background-color:black;color:lime}
+.G1 {background-color:black;color:lime}
+.S1 {background-color:black;color:lime}
+.T1 {background-color:black;color:lime}
+.C1 {background-color:black;color:orange}
+.P1 {background-color:black;color:aqua}
+.D1 {background-color:black;color:white}
+.E1 {background-color:black;color:white}
+.Q1 {background-color:black;color:white}
+.N1 {background-color:black;color:white}
+.F1 {background-color:black;color:yellow}
+.W1 {background-color:black;color:yellow}
+.Y1 {background-color:black;color:yellow}
+.H1 {background-color:black;color:red}
+.K1 {background-color:black;color:red}
+.R1 {background-color:black;color:red}
+.I1 {background-color:black;color:fuchsia}
+.L1 {background-color:black;color:fuchsia}
+.M1 {background-color:black;color:fuchsia}
+.V1 {background-color:black;color:fuchsia}
+--></style>
+</head>
+
+<body bgcolor=#f5f5a3>
+<h2>Gblocks 0.91b Results</h2>
+<p>
+Processed file: <b>input.pir</b><br>
+Number of sequences: <b>17</b><br>Alignment assumed to be: <b>Protein</b><br>
+New number of positions: <b>56</b> (selected positions are underlined in blue)
+</p>
+<pre>
+                         10        20        30        40        50        60
+                 =========+=========+=========+=========+=========+=========+
+nad3_parde       ------MEYLLQEYLPI<span class=L1>L</span>VFLGMASA<span class=L1>L</span>AIV<span class=L1>L</span>ILAAAVIAVRN--PDP<span class=E1>E</span><span class=K1>K</span>V<span class=S1>S</span>A<span class=Y1>Y</span><span class=E1>E</span><span class=C1>C</span><span class=G1>G</span><span class=F1>F</span>NA<span class=F1>F</span>
+nad3_acaca       ---------MTLEYIYIFIFFWGAFFI<span class=S1>S</span>CL<span class=L1>L</span>IFLSYF<span class=L1>L</span>VYQE--SDI<span class=E1>E</span><span class=K1>K</span>N<span class=S1>S</span>A<span class=Y1>Y</span><span class=E1>E</span><span class=C1>C</span><span class=G1>G</span><span class=F1>F</span>Q<span class=P1>P</span><span class=F1>F</span>
+nad3_allma       --------------MTY<span class=L1>L</span>VYIVFTIV<span class=L1>L</span>TVG<span class=L1>L</span>ILVSYL<span class=L1>L</span>SQAQ--PDS<span class=E1>E</span><span class=K1>K</span>V<span class=S1>S</span>A<span class=Y1>Y</span><span class=E1>E</span><span class=C1>C</span><span class=G1>G</span><span class=F1>F</span>S<span class=P1>P</span>L
+nad3_apec        -----------IFNFLT<span class=L1>L</span>FVSILIFLITTLITFAAHF<span class=L1>L</span>PSRN-TD-S<span class=E1>E</span><span class=K1>K</span>S<span class=S1>S</span>P<span class=Y1>Y</span><span class=E1>E</span><span class=C1>C</span><span class=G1>G</span><span class=F1>F</span><span class=D1>D</span><span class=P1>P</span>L
+nad3_arath       ---------MMSEFAPISIYLVISLLV<span class=S1>S</span>LI<span class=L1>L</span>LGVPFPFASNS-STYP<span class=E1>E</span><span class=K1>K</span>L<span class=S1>S</span>A<span class=Y1>Y</span><span class=E1>E</span><span class=C1>C</span><span class=G1>G</span><span class=F1>F</span><span class=D1>D</span><span class=P1>P</span>S
+nad3_balca       -------------MNSF<span class=L1>L</span>IYLLIAIT<span class=L1>L</span><span class=S1>S</span>FI<span class=L1>L</span>SIVGHR<span class=L1>L</span>PTRN-MD-Q<span class=E1>E</span><span class=K1>K</span>L<span class=S1>S</span>P<span class=Y1>Y</span><span class=E1>E</span><span class=C1>C</span><span class=G1>G</span><span class=F1>F</span><span class=D1>D</span><span class=P1>P</span>Q
+nad3_chocr       ------MKLIFTEYSAI<span class=L1>L</span>IFFAISSL<span class=L1>L</span><span class=S1>S</span>SVIFLLSYF<span class=L1>L</span>IPQK--PDQ<span class=E1>E</span><span class=K1>K</span>V<span class=S1>S</span>A<span class=Y1>Y</span><span class=E1>E</span><span class=C1>C</span><span class=G1>G</span><span class=F1>F</span>N<span class=P1>P</span><span class=F1>F</span>
+nad3_drome       -------------MFSIIFIALLILLITTIVMFLASI<span class=L1>L</span>SKKA-LIDR<span class=E1>E</span><span class=K1>K</span>S<span class=S1>S</span>PF<span class=E1>E</span><span class=C1>C</span><span class=G1>G</span><span class=F1>F</span><span class=D1>D</span><span class=P1>P</span>K
+nad3_human       -------------MN-FALILMINTL<span class=L1>L</span>ALL<span class=L1>L</span>MIITFW<span class=L1>L</span>PQLN-GY-M<span class=E1>E</span><span class=K1>K</span>STP<span class=Y1>Y</span><span class=E1>E</span><span class=C1>C</span><span class=G1>G</span><span class=F1>F</span><span class=D1>D</span><span class=P1>P</span>M
+nad3_ktun        -------------MFFV<span class=L1>L</span>SLVLFTFL<span class=L1>L</span><span class=S1>S</span>LV<span class=L1>L</span>LSVSLS<span class=L1>L</span>TKKK-MMNR<span class=E1>E</span><span class=K1>K</span>S<span class=S1>S</span>PF<span class=E1>E</span><span class=C1>C</span><span class=G1>G</span><span class=F1>F</span><span class=D1>D</span><span class=P1>P</span>K
+nad3_lter        -------------MILTALSSAIALLVPIIILGAAWV<span class=L1>L</span>ASRS-TEDR<span class=E1>E</span><span class=K1>K</span>S<span class=S1>S</span>PF<span class=E1>E</span><span class=C1>C</span><span class=G1>G</span><span class=F1>F</span><span class=D1>D</span><span class=P1>P</span>K
+nad3_marpo       -----------MEFAPIFVYLVISLL<span class=L1>L</span><span class=S1>S</span>LI<span class=L1>L</span>IGVSFLFASSSSLAYP<span class=E1>E</span><span class=K1>K</span>L<span class=S1>S</span>A<span class=Y1>Y</span><span class=E1>E</span><span class=C1>C</span><span class=G1>G</span><span class=F1>F</span><span class=D1>D</span><span class=P1>P</span><span class=F1>F</span>
+nad3_metse       ---------MYTEFYGI<span class=L1>L</span>VLLIFSVV<span class=L1>L</span><span class=S1>S</span>AIISGASYI<span class=L1>L</span>GDKQ--PDR<span class=E1>E</span><span class=K1>K</span>V<span class=S1>S</span>A<span class=Y1>Y</span><span class=E1>E</span><span class=C1>C</span><span class=G1>G</span><span class=F1>F</span><span class=D1>D</span><span class=P1>P</span><span class=F1>F</span>
+nad3_picca       MLNYFVYPYGIENDMGMKFYMMLVPMM<span class=S1>S</span>MV<span class=L1>L</span>MMINYMMTNKS-DNNMN<span class=K1>K</span>TGP<span class=Y1>Y</span><span class=E1>E</span><span class=C1>C</span><span class=G1>G</span><span class=F1>F</span><span class=D1>D</span>S<span class=F1>F</span>
+nad3_podan       -------------MSSMTLFILFVSIIALLFLFINLIFAPHN--PYQ<span class=E1>E</span><span class=K1>K</span>Y<span class=S1>S</span>IF<span class=E1>E</span><span class=C1>C</span><span class=G1>G</span><span class=F1>F</span>HS<span class=F1>F</span>
+nad3_prowi       ----------MYEFLGI<span class=L1>L</span>IYFFIALA<span class=L1>L</span><span class=S1>S</span>LL<span class=L1>L</span>LGLPFLVSTRK--ADP<span class=E1>E</span><span class=K1>K</span>I<span class=S1>S</span>A<span class=Y1>Y</span><span class=E1>E</span><span class=C1>C</span><span class=G1>G</span><span class=F1>F</span><span class=D1>D</span><span class=P1>P</span><span class=F1>F</span>
+nad3_recam       -----MNTMILSEYLSV<span class=L1>L</span>IFFIFSFG<span class=L1>L</span><span class=S1>S</span>CIILGLSYV<span class=L1>L</span>ATQN--ADT<span class=E1>E</span><span class=K1>K</span>L<span class=S1>S</span>P<span class=Y1>Y</span><span class=E1>E</span><span class=C1>C</span><span class=G1>G</span><span class=F1>F</span>N<span class=P1>P</span><span class=F1>F</span>
+                                                                <span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span>
+
+
+                         70        80        90       100       110       120
+                 =========+=========+=========+=========+=========+=========+
+nad3_parde       D-D<span class=A1>A</span><span class=R1>R</span>MK<span class=F1>F</span>DV<span class=R1>R</span><span class=F1>F</span>Y<span class=L1>L</span><span class=V1>V</span>S<span class=I1>I</span><span class=L1>L</span><span class=F1>F</span>I<span class=I1>I</span><span class=F1>F</span><span class=D1>D</span><span class=L1>L</span><span class=E1>E</span>VAF<span class=L1>L</span><span class=F1>F</span><span class=P1>P</span>WAVSFASLS-DVAF<span class=W1>W</span>GLMVFLAV<span class=L1>L</span><span class=T1>T</span>V<span class=G1>G</span><span class=F1>F</span>A
+nad3_acaca       E-DT<span class=R1>R</span>SK<span class=F1>F</span>NV<span class=R1>R</span>YY<span class=L1>L</span>I<span class=A1>A</span><span class=I1>I</span><span class=L1>L</span><span class=F1>F</span>M<span class=I1>I</span><span class=F1>F</span><span class=D1>D</span><span class=L1>L</span><span class=E1>E</span><span class=I1>I</span>MY<span class=L1>L</span><span class=F1>F</span><span class=P1>P</span>WSISISTGS-FFGV<span class=W1>W</span>AIFLFLI<span class=I1>I</span><span class=L1>L</span><span class=T1>T</span>V<span class=G1>G</span><span class=F1>F</span><span class=I1>I</span>
+nad3_allma       G-D<span class=A1>A</span><span class=R1>R</span>QK<span class=F1>F</span>DVS<span class=F1>F</span>Y<span class=L1>L</span>I<span class=A1>A</span><span class=I1>I</span><span class=L1>L</span><span class=F1>F</span>I<span class=I1>I</span><span class=F1>F</span><span class=D1>D</span><span class=L1>L</span><span class=E1>E</span>VVFIL<span class=P1>P</span>FASVIHNVS-LLGG<span class=W1>W</span>ITIIFLV<span class=I1>I</span><span class=L1>L</span><span class=T1>T</span><span class=I1>I</span><span class=G1>G</span><span class=F1>F</span><span class=I1>I</span>
+nad3_apec        N-S<span class=A1>A</span><span class=R1>R</span>VP<span class=F1>F</span>SF<span class=R1>R</span><span class=F1>F</span>F<span class=L1>L</span><span class=V1>V</span><span class=A1>A</span><span class=I1>I</span><span class=L1>L</span><span class=F1>F</span><span class=L1>L</span>L<span class=F1>F</span><span class=D1>D</span><span class=L1>L</span><span class=E1>E</span><span class=I1>I</span>AL<span class=L1>L</span><span class=F1>F</span><span class=P1>P</span>LPFSVFFH--P--IHTP----L<span class=I1>I</span><span class=L1>L</span><span class=T1>T</span>V<span class=G1>G</span>L<span class=I1>I</span>
+nad3_arath       G-D<span class=A1>A</span><span class=R1>R</span>SR<span class=F1>F</span>DI<span class=R1>R</span><span class=F1>F</span>Y<span class=L1>L</span><span class=V1>V</span>S<span class=I1>I</span><span class=L1>L</span><span class=F1>F</span><span class=L1>L</span><span class=I1>I</span>P<span class=D1>D</span><span class=L1>L</span><span class=E1>E</span>VTFF<span class=F1>F</span><span class=P1>P</span>WAVPPNKID-LFGF<span class=W1>W</span>SMMAFLF<span class=I1>I</span><span class=L1>L</span><span class=T1>T</span><span class=I1>I</span><span class=G1>G</span><span class=F1>F</span>L
+nad3_balca       A-S<span class=A1>A</span><span class=R1>R</span>LP<span class=F1>F</span>SL<span class=R1>R</span><span class=F1>F</span>F<span class=L1>L</span><span class=V1>V</span><span class=A1>A</span><span class=I1>I</span><span class=L1>L</span><span class=F1>F</span><span class=L1>L</span>L<span class=F1>F</span><span class=D1>D</span><span class=L1>L</span><span class=E1>E</span><span class=I1>I</span>AL<span class=L1>L</span>L<span class=P1>P</span>FPAALSARDPQLSFTLAFLILL<span class=I1>I</span><span class=L1>L</span><span class=T1>T</span><span class=I1>I</span><span class=G1>G</span>L<span class=I1>I</span>
+nad3_chocr       D-D<span class=A1>A</span><span class=R1>R</span>AT<span class=F1>F</span>DI<span class=R1>R</span><span class=F1>F</span>Y<span class=L1>L</span><span class=V1>V</span><span class=A1>A</span><span class=I1>I</span><span class=L1>L</span><span class=F1>F</span><span class=L1>L</span><span class=I1>I</span><span class=F1>F</span><span class=D1>D</span><span class=L1>L</span><span class=E1>E</span><span class=I1>I</span>SF<span class=L1>L</span><span class=F1>F</span><span class=P1>P</span>WSLVLGEIS-IIGF<span class=W1>W</span>SMIVFLV<span class=I1>I</span><span class=L1>L</span><span class=T1>T</span><span class=I1>I</span><span class=G1>G</span><span class=F1>F</span><span class=I1>I</span>
+nad3_drome       S-SS<span class=R1>R</span>LP<span class=F1>F</span>SL<span class=R1>R</span><span class=F1>F</span>F<span class=L1>L</span>IT<span class=I1>I</span>I<span class=F1>F</span><span class=L1>L</span><span class=I1>I</span><span class=F1>F</span><span class=D1>D</span>V<span class=E1>E</span><span class=I1>I</span>ALIL<span class=P1>P</span>MIIIMKYSNIMIWTITSIIFIL<span class=I1>I</span><span class=L1>L</span>L<span class=I1>I</span><span class=G1>G</span>LY
+nad3_human       S-P<span class=A1>A</span><span class=R1>R</span>VP<span class=F1>F</span>SMK<span class=F1>F</span>F<span class=L1>L</span><span class=V1>V</span><span class=A1>A</span><span class=I1>I</span>T<span class=F1>F</span><span class=L1>L</span>L<span class=F1>F</span><span class=D1>D</span><span class=L1>L</span><span class=E1>E</span><span class=I1>I</span>AL<span class=L1>L</span>L<span class=P1>P</span>LPWALQTTNLPLMVMSSLLLII<span class=I1>I</span><span class=L1>L</span>ALSLA
+nad3_ktun        S-S<span class=A1>A</span><span class=R1>R</span>LP<span class=F1>F</span>SM<span class=R1>R</span><span class=F1>F</span>F<span class=L1>L</span>ITVV<span class=F1>F</span><span class=L1>L</span>V<span class=F1>F</span><span class=D1>D</span>V<span class=E1>E</span><span class=I1>I</span>VL<span class=L1>L</span>L<span class=P1>P</span>YLFSSGWSIDVFSLVGSMMILV<span class=I1>I</span><span class=L1>L</span>I<span class=I1>I</span><span class=G1>G</span>VL
+nad3_lter        S-T<span class=A1>A</span><span class=R1>R</span>IP<span class=F1>F</span>ST<span class=R1>R</span><span class=F1>F</span>F<span class=L1>L</span>L<span class=A1>A</span><span class=I1>I</span>I<span class=F1>F</span>IV<span class=F1>F</span><span class=D1>D</span>I<span class=E1>E</span><span class=I1>I</span>VL<span class=L1>L</span>M<span class=P1>P</span>LPTILHTSDVFTTVTTSVLFLM<span class=I1>I</span><span class=L1>L</span>L<span class=I1>I</span><span class=G1>G</span>L<span class=I1>I</span>
+nad3_marpo       D-D<span class=A1>A</span><span class=R1>R</span>SR<span class=F1>F</span>DI<span class=R1>R</span><span class=F1>F</span>Y<span class=L1>L</span><span class=V1>V</span>S<span class=I1>I</span><span class=L1>L</span><span class=F1>F</span>I<span class=I1>I</span><span class=F1>F</span><span class=D1>D</span><span class=L1>L</span><span class=E1>E</span>VTF<span class=L1>L</span><span class=F1>F</span><span class=P1>P</span>WAVSLNKIG-LFGF<span class=W1>W</span>SMMVFLF<span class=I1>I</span><span class=L1>L</span><span class=T1>T</span><span class=I1>I</span><span class=G1>G</span><span class=F1>F</span>V
+nad3_metse       G-TPGRP<span class=F1>F</span>SI<span class=R1>R</span><span class=F1>F</span>F<span class=L1>L</span>IG<span class=I1>I</span><span class=L1>L</span><span class=F1>F</span><span class=L1>L</span><span class=I1>I</span><span class=F1>F</span><span class=D1>D</span><span class=L1>L</span><span class=E1>E</span><span class=I1>I</span>SF<span class=L1>L</span><span class=F1>F</span><span class=P1>P</span>WCVVCNQVF-PFGY<span class=W1>W</span>TMIVFLAV<span class=L1>L</span><span class=T1>T</span>L<span class=G1>G</span>LV
+nad3_picca       R-QS<span class=R1>R</span>TTYSIK<span class=F1>F</span>I<span class=L1>L</span>I<span class=A1>A</span><span class=I1>I</span><span class=L1>L</span><span class=F1>F</span><span class=L1>L</span>P<span class=F1>F</span><span class=D1>D</span><span class=L1>L</span><span class=E1>E</span>LTSIL<span class=P1>P</span>YTLSMYNTN-IYGLFILLYFLLP<span class=L1>L</span>I<span class=I1>I</span><span class=G1>G</span><span class=F1>F</span><span class=I1>I</span>
+nad3_podan       LGQN<span class=R1>R</span>TQ<span class=F1>F</span>GVK<span class=F1>F</span>FIF<span class=A1>A</span>LVY<span class=L1>L</span>LL<span class=D1>D</span><span class=L1>L</span><span class=E1>E</span><span class=I1>I</span>LLT<span class=F1>F</span><span class=P1>P</span>FAVSEYVNN-IYGLIILLGFIT<span class=I1>I</span>I<span class=T1>T</span><span class=I1>I</span><span class=G1>G</span><span class=F1>F</span>V
+nad3_prowi       D-D<span class=A1>A</span><span class=R1>R</span>GR<span class=F1>F</span>DIQ<span class=F1>F</span>Y<span class=L1>L</span><span class=V1>V</span><span class=A1>A</span><span class=I1>I</span><span class=L1>L</span><span class=F1>F</span>I<span class=I1>I</span><span class=F1>F</span><span class=D1>D</span><span class=L1>L</span><span class=E1>E</span>VAF<span class=L1>L</span><span class=F1>F</span><span class=P1>P</span>WALTLNKIG-YFGF<span class=W1>W</span>SMMLFLF<span class=I1>I</span><span class=L1>L</span><span class=T1>T</span>V<span class=G1>G</span><span class=F1>F</span><span class=I1>I</span>
+nad3_recam       D-D<span class=A1>A</span><span class=R1>R</span>GA<span class=F1>F</span>DV<span class=R1>R</span><span class=F1>F</span>Y<span class=L1>L</span><span class=V1>V</span><span class=A1>A</span><span class=I1>I</span><span class=L1>L</span><span class=F1>F</span>I<span class=I1>I</span><span class=F1>F</span><span class=D1>D</span><span class=L1>L</span><span class=E1>E</span>VAF<span class=L1>L</span><span class=F1>F</span><span class=P1>P</span>WAVALSDVT-IFGF<span class=W1>W</span>TMFIFLL<span class=I1>I</span><span class=L1>L</span><span class=T1>T</span>V<span class=G1>G</span><span class=F1>F</span><span class=I1>I</span>
+                    <span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span>                      <span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span>
+
+
+                        130       140       150
+                 =========+=========+=========+===
+nad3_parde       <span class=Y1>Y</span><span class=E1>E</span><span class=W1>W</span>KK<span class=G1>G</span><span class=A1>A</span><span class=L1>L</span>E<span class=W1>W</span>A----------------------
+nad3_acaca       <span class=Y1>Y</span><span class=E1>E</span><span class=W1>W</span>QK<span class=G1>G</span><span class=A1>A</span><span class=L1>L</span>E<span class=W1>W</span>D----------------------
+nad3_allma       <span class=Y1>Y</span><span class=E1>E</span>FVS<span class=G1>G</span><span class=A1>A</span>ITDSF---------------------
+nad3_apec        F<span class=E1>E</span><span class=W1>W</span>VQ<span class=G1>G</span>G<span class=L1>L</span>D<span class=W1>W</span>AE---------------------
+nad3_arath       <span class=Y1>Y</span><span class=E1>E</span><span class=W1>W</span>KR<span class=G1>G</span><span class=A1>A</span>SDRE----------------------
+nad3_balca       <span class=Y1>Y</span><span class=E1>E</span><span class=W1>W</span>ME<span class=G1>G</span>G<span class=L1>L</span>E<span class=W1>W</span>AE---------------------
+nad3_chocr       <span class=Y1>Y</span><span class=E1>E</span><span class=W1>W</span>YK<span class=G1>G</span><span class=A1>A</span><span class=L1>L</span>E<span class=W1>W</span>E----------------------
+nad3_drome       H<span class=E1>E</span><span class=W1>W</span>NQ<span class=G1>G</span>M<span class=L1>L</span>N<span class=W1>W</span>SN---------------------
+nad3_human       <span class=Y1>Y</span><span class=E1>E</span><span class=W1>W</span>LQKG<span class=L1>L</span>D<span class=W1>W</span>TE---------------------
+nad3_ktun        H<span class=E1>E</span><span class=W1>W</span>SE<span class=G1>G</span>S<span class=L1>L</span>E<span class=W1>W</span>FSSSN------------------
+nad3_lter        H<span class=E1>E</span><span class=W1>W</span>KE<span class=G1>G</span>S<span class=L1>L</span>D<span class=W1>W</span>SS---------------------
+nad3_marpo       <span class=Y1>Y</span><span class=E1>E</span><span class=W1>W</span>KK<span class=G1>G</span><span class=A1>A</span><span class=L1>L</span>D<span class=W1>W</span>E----------------------
+nad3_metse       <span class=Y1>Y</span><span class=E1>E</span><span class=W1>W</span>LK<span class=G1>G</span>G<span class=L1>L</span>E<span class=W1>W</span>E----------------------
+nad3_picca       I<span class=E1>E</span>INTK<span class=A1>A</span>IYMTKMFNRNVKSMTSYVKYNNKI--
+nad3_podan       <span class=Y1>Y</span><span class=E1>E</span>LGKS<span class=A1>A</span><span class=L1>L</span>KIDSRQVITMTRFNYSSTIEYLGKI
+nad3_prowi       <span class=Y1>Y</span><span class=E1>E</span><span class=W1>W</span>RK<span class=G1>G</span><span class=A1>A</span><span class=L1>L</span>D<span class=W1>W</span>S----------------------
+nad3_recam       <span class=Y1>Y</span><span class=E1>E</span><span class=W1>W</span>KK<span class=G1>G</span><span class=A1>A</span><span class=L1>L</span>D<span class=W1>W</span>E----------------------
+                 <span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span><span class=BL>#</span>                         
+
+
+
+</pre>
+<pre>
+
+
+<br><b>Parameters used</b>
+Minimum Number Of Sequences For A Conserved Position: 9
+Minimum Number Of Sequences For A Flanking Position: 14
+Maximum Number Of Contiguous Nonconserved Positions: 8
+Minimum Length Of A Block: 10
+Allowed Gap Positions: None
+Use Similarity Matrices: Yes
+
+</pre><pre><b>Flank positions of the 3 selected block(s)</b>
+Flanks: [48  60]  [64  91]  [114  128]  
+
+New number of positions in input.pir-gb: <b> 56 </b> (36% of the original 153 positions)
+
+
+</body>
+</html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Gblocks_Selected_Blocks_on_data_95.txt	Thu Apr 12 06:59:23 2018 -0400
@@ -0,0 +1,68 @@
+>P1;nad3_parde
+ 
+EKVSAYECGF NAFARMKFDV RFYLVSILFI IFDLEVAFLF PVLTVGFAYE WKKGAL*
+
+>P1;nad3_acaca
+ 
+EKNSAYECGF QPFTRSKFNV RYYLIAILFM IFDLEIMYLF PILTVGFIYE WQKGAL*
+
+>P1;nad3_allma
+ 
+EKVSAYECGF SPLARQKFDV SFYLIAILFI IFDLEVVFIL PILTIGFIYE FVSGAI*
+
+>P1;nad3_apec
+ 
+EKSSPYECGF DPLARVPFSF RFFLVAILFL LFDLEIALLF PILTVGLIFE WVQGGL*
+
+>P1;nad3_arath
+ 
+EKLSAYECGF DPSARSRFDI RFYLVSILFL IPDLEVTFFF PILTIGFLYE WKRGAS*
+
+>P1;nad3_balca
+ 
+EKLSPYECGF DPQARLPFSL RFFLVAILFL LFDLEIALLL PILTIGLIYE WMEGGL*
+
+>P1;nad3_chocr
+ 
+EKVSAYECGF NPFARATFDI RFYLVAILFL IFDLEISFLF PILTIGFIYE WYKGAL*
+
+>P1;nad3_drome
+ 
+EKSSPFECGF DPKSRLPFSL RFFLITIIFL IFDVEIALIL PILLIGLYHE WNQGML*
+
+>P1;nad3_human
+ 
+EKSTPYECGF DPMARVPFSM KFFLVAITFL LFDLEIALLL PILALSLAYE WLQKGL*
+
+>P1;nad3_ktun
+ 
+EKSSPFECGF DPKARLPFSM RFFLITVVFL VFDVEIVLLL PILIIGVLHE WSEGSL*
+
+>P1;nad3_lter
+ 
+EKSSPFECGF DPKARIPFST RFFLLAIIFI VFDIEIVLLM PILLIGLIHE WKEGSL*
+
+>P1;nad3_marpo
+ 
+EKLSAYECGF DPFARSRFDI RFYLVSILFI IFDLEVTFLF PILTIGFVYE WKKGAL*
+
+>P1;nad3_metse
+ 
+EKVSAYECGF DPFPGRPFSI RFFLIGILFL IFDLEISFLF PVLTLGLVYE WLKGGL*
+
+>P1;nad3_picca
+ 
+NKTGPYECGF DSFSRTTYSI KFILIAILFL PFDLELTSIL PPLIIGFIIE INTKAI*
+
+>P1;nad3_podan
+ 
+EKYSIFECGF HSFNRTQFGV KFFIFALVYL LLDLEILLTF PIITIGFVYE LGKSAL*
+
+>P1;nad3_prowi
+ 
+EKISAYECGF DPFARGRFDI QFYLVAILFI IFDLEVAFLF PILTVGFIYE WRKGAL*
+
+>P1;nad3_recam
+ 
+EKLSPYECGF NPFARGAFDV RFYLVAILFI IFDLEVAFLF PILTVGFIYE WKKGAL*
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Gblocks_on_data_95.txt	Thu Apr 12 06:59:23 2018 -0400
@@ -0,0 +1,8 @@
+
+17 sequences and 153 positions in the first alignment file:
+input.pir
+
+input.pir
+Original alignment: 153 positions
+Gblocks alignment:  56 positions (36 %) in 3 selected block(s)
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nad3.fasta	Thu Apr 12 06:59:23 2018 -0400
@@ -0,0 +1,101 @@
+>P1;nad3_parde
+
+------MEYLLQEYLPILVFLGMASALAIVLILAAAVIAVRN--PDPEKVSAYECGFNAF
+D-DARMKFDVRFYLVSILFIIFDLEVAFLFPWAVSFASLS-DVAFWGLMVFLAVLTVGFA
+YEWKKGALEWA----------------------*
+
+>P1;nad3_acaca
+
+---------MTLEYIYIFIFFWGAFFISCLLIFLSYFLVYQE--SDIEKNSAYECGFQPF
+E-DTRSKFNVRYYLIAILFMIFDLEIMYLFPWSISISTGS-FFGVWAIFLFLIILTVGFI
+YEWQKGALEWD----------------------*
+
+>P1;nad3_allma
+
+--------------MTYLVYIVFTIVLTVGLILVSYLLSQAQ--PDSEKVSAYECGFSPL
+G-DARQKFDVSFYLIAILFIIFDLEVVFILPFASVIHNVS-LLGGWITIIFLVILTIGFI
+YEFVSGAITDSF---------------------*
+
+>P1;nad3_apec
+
+-----------IFNFLTLFVSILIFLITTLITFAAHFLPSRN-TD-SEKSSPYECGFDPL
+N-SARVPFSFRFFLVAILFLLFDLEIALLFPLPFSVFFH--P--IHTP----LILTVGLI
+FEWVQGGLDWAE---------------------*
+
+>P1;nad3_arath
+
+---------MMSEFAPISIYLVISLLVSLILLGVPFPFASNS-STYPEKLSAYECGFDPS
+G-DARSRFDIRFYLVSILFLIPDLEVTFFFPWAVPPNKID-LFGFWSMMAFLFILTIGFL
+YEWKRGASDRE----------------------*
+
+>P1;nad3_balca
+
+-------------MNSFLIYLLIAITLSFILSIVGHRLPTRN-MD-QEKLSPYECGFDPQ
+A-SARLPFSLRFFLVAILFLLFDLEIALLLPFPAALSARDPQLSFTLAFLILLILTIGLI
+YEWMEGGLEWAE---------------------*
+
+>P1;nad3_chocr
+
+------MKLIFTEYSAILIFFAISSLLSSVIFLLSYFLIPQK--PDQEKVSAYECGFNPF
+D-DARATFDIRFYLVAILFLIFDLEISFLFPWSLVLGEIS-IIGFWSMIVFLVILTIGFI
+YEWYKGALEWE----------------------*
+
+>P1;nad3_drome
+
+-------------MFSIIFIALLILLITTIVMFLASILSKKA-LIDREKSSPFECGFDPK
+S-SSRLPFSLRFFLITIIFLIFDVEIALILPMIIIMKYSNIMIWTITSIIFILILLIGLY
+HEWNQGMLNWSN---------------------*
+
+>P1;nad3_human
+
+-------------MN-FALILMINTLLALLLMIITFWLPQLN-GY-MEKSTPYECGFDPM
+S-PARVPFSMKFFLVAITFLLFDLEIALLLPLPWALQTTNLPLMVMSSLLLIIILALSLA
+YEWLQKGLDWTE---------------------*
+
+>P1;nad3_ktun
+
+-------------MFFVLSLVLFTFLLSLVLLSVSLSLTKKK-MMNREKSSPFECGFDPK
+S-SARLPFSMRFFLITVVFLVFDVEIVLLLPYLFSSGWSIDVFSLVGSMMILVILIIGVL
+HEWSEGSLEWFSSSN------------------*
+
+>P1;nad3_lter
+
+-------------MILTALSSAIALLVPIIILGAAWVLASRS-TEDREKSSPFECGFDPK
+S-TARIPFSTRFFLLAIIFIVFDIEIVLLMPLPTILHTSDVFTTVTTSVLFLMILLIGLI
+HEWKEGSLDWSS---------------------*
+
+>P1;nad3_marpo
+
+-----------MEFAPIFVYLVISLLLSLILIGVSFLFASSSSLAYPEKLSAYECGFDPF
+D-DARSRFDIRFYLVSILFIIFDLEVTFLFPWAVSLNKIG-LFGFWSMMVFLFILTIGFV
+YEWKKGALDWE----------------------*
+
+>P1;nad3_metse
+
+---------MYTEFYGILVLLIFSVVLSAIISGASYILGDKQ--PDREKVSAYECGFDPF
+G-TPGRPFSIRFFLIGILFLIFDLEISFLFPWCVVCNQVF-PFGYWTMIVFLAVLTLGLV
+YEWLKGGLEWE----------------------*
+
+>P1;nad3_picca
+
+MLNYFVYPYGIENDMGMKFYMMLVPMMSMVLMMINYMMTNKS-DNNMNKTGPYECGFDSF
+R-QSRTTYSIKFILIAILFLPFDLELTSILPYTLSMYNTN-IYGLFILLYFLLPLIIGFI
+IEINTKAIYMTKMFNRNVKSMTSYVKYNNKI--*
+
+>P1;nad3_podan
+
+-------------MSSMTLFILFVSIIALLFLFINLIFAPHN--PYQEKYSIFECGFHSF
+LGQNRTQFGVKFFIFALVYLLLDLEILLTFPFAVSEYVNN-IYGLIILLGFITIITIGFV
+YELGKSALKIDSRQVITMTRFNYSSTIEYLGKI*
+
+>P1;nad3_prowi
+
+----------MYEFLGILIYFFIALALSLLLLGLPFLVSTRK--ADPEKISAYECGFDPF
+D-DARGRFDIQFYLVAILFIIFDLEVAFLFPWALTLNKIG-YFGFWSMMLFLFILTVGFI
+YEWRKGALDWS----------------------*
+
+>P1;nad3_recam
+
+-----MNTMILSEYLSVLIFFIFSFGLSCIILGLSYVLATQN--ADTEKLSPYECGFNPF
+D-DARGAFDVRFYLVAILFIIFDLEVAFLFPWAVALSDVT-IFGFWTMFIFLLILTVGFI
+YEWKKGALDWE----------------------*