# HG changeset patch
# User iuc
# Date 1566586033 14400
# Node ID cd9d1eccda7e1a8e5f4f9ce6d645e8c31e5e0a0b

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"

diff -r 000000000000 -r cd9d1eccda7e pipelign.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pipelign.xml	Fri Aug 23 14:47:13 2019 -0400
@@ -0,0 +1,87 @@
+<?xml version="1.0"?>
+<tool id="pipelign" name="Automated multiple sequence" version="@VERSION@+galaxy0">
+    <description>alignment with pipelign</description>
+    <macros>
+        <token name="@VERSION@">0.2</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">pipelign</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        pipelign
+            --outDir files
+            --clearExistingDirectory
+            --inFile '$inFile'
+            --outFile '$outFile'
+            --lenThr $lenThr
+            --alphabet $alphabet
+            --simPer $simPer
+            --merge $merge
+            --thread \${GALAXY_SLOTS:-1}
+            --mIterateLong $mIterateLong
+            --mIterateMerge $mIterateMerge
+            --ambigPer $ambigPer
+            $keepOrphans $keepBadSeqs $excludeClusters
+    ]]></command>
+    <inputs>
+        <param argument="--inFile" type="data" format="fasta" label="Input sequence file" />
+        <param argument="--lenThr" type="float" value="0.7" min="0" max="1" label="Length threshold for full sequences" help="Default: 0.7" />
+        <param argument="--alphabet" type="select" label="Alphabet for input sequences">
+            <option value="dna">DNA</option>
+            <option value="rna">RNA</option>
+            <option value="aa">Amino Acids</option>
+        </param>
+        <param argument="--keepOrphans" type="boolean" truevalue="--keepOrphans" falsevalue="" label="Add fragments without clusters" />
+        <param argument="--keepBadSeqs" type="boolean" truevalue="--keepBadSeqs" falsevalue="" label="Add long sequences with too many ambiguous residues" />
+        <param argument="--simPer" type="float" value="0.8" min="0" max="1" label="Percent sequence similarity for clustering" />
+        <param argument="--merge" type="select" label="Merge strategy">
+            <option value="P">Parallel</option>
+            <option value="C">Consensus</option>
+        </param>
+        <param argument="--mIterateLong" type="integer" value="1" min="1" label="Number of iterations to refine long alignments" />
+        <param argument="--mIterateMerge" type="integer" value="1" min="1" label="Number of iterations to refine merged alignment" />
+        <param argument="--ambigPer" type="float" value="0.1" min="0" max="1" label="Percent sequence similarity for clustering" />
+        <param argument="--excludeClusters" type="boolean" truevalue="--excludeClusters" falsevalue="" label="Exclude clusters from final alignment" />
+    </inputs>
+    <outputs>
+        <data name="outFile" format="fasta" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="inFile" value="pipelign-in1.fasta" />
+            <output name="outFile">
+                <assert_contents>
+                    <has_line line="&gt;K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1" />
+                    <has_line line="&gt;K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1" />
+                    <has_line line="&gt;K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1" />
+                    <has_line line="&gt;K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1" />
+                    <has_line line="&gt;K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1" />
+                    <has_line line="&gt;K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1" />
+                    <has_line line="&gt;K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1" />
+                    <has_line line="&gt;K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+-------------------
+
+A pipeline for automated multiple sequence alignment, particularly of viral sequences.
+
+]]>
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @UNPUBLISHED{spond,
+                author = "A.S.Md.M. Hossain, S.D.W.Frost",
+                title = "Pipelign: an alignment pipeline for viral sequences.",
+                year = "2019",
+                note = "https://github.com/asmmhossain/pipelign/",
+                url = "https://github.com/asmmhossain/pipelign/"}
+        </citation>
+    </citations>
+</tool>
diff -r 000000000000 -r cd9d1eccda7e test-data/pipelign-in1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pipelign-in1.fasta	Fri Aug 23 14:47:13 2019 -0400
@@ -0,0 +1,200 @@
+>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1
+CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAA
+>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1
+GAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCAATCAAATCAG
+>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1
+ATCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCTGTCACATTTACCAATACT
+>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1
+CTATGTTTACTTCTAATCCCGAATCCTGCAAAGCTAGATAAATTGCTTGTAACTCAGTCTTCTGATTTGT
+>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1
+CCAAGTATCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATCCTAGGAAAATGTCTA
+>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1
+CTACTATTGCTACTAATGGTATAGGTTGCGTTACATGTACTACTTACTGCTTTGATAGAGAAGCTTGATG
+>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1
+TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATAATTCCCTTCT
+>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1
+AATAGCAATTTGTACAAGCAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGGCTCTCGTCTAGGATCAAC
+>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1
+ACAACGGAATTGGAGGAAATGAACCAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTT
+>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1
+AGGATTTTACATAATTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAATTTCCCCACTA
+>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1
+TTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTACACCCAGTGGGGGGACATCAAGCAGCCA
+>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1
+CTACCTCTTCTTCTGCTAGACTGCCATTTAACAGCAGTTGAGTTGATACTACTGGCCTAATTCCATGTGT
+>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1
+TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTTATGGCAAATACTGGAGTATTG
+>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1
+CTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTGTA
+>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1
+TGCCAAGGATCCGTTCACTAATCGAATGGATCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCT
+>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1
+CAGGATTAACTGCGAATCTTTCTAGCTCCCTTGTTGCCCATACTATATGTTTTAATTTATATTTTTTCTT
+>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1
+GCTGCTCCCACCCTATCTTGTGCTGGCTCAGCTCGTCTCATTGTTTCCCTTACAGTAGGCCATCCAATCA
+>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1
+ACAGTAGAAAAATTCCCCTCCACCATTAAAACTGTGGTTACAATATCTGGGTCCCCTCCTGAGGATTGGT
+>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1
+TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATC
+>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1
+AGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGGATTAGAACATGG
+>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1
+GATCCTGCATATAAGCAGCAGCTTTTTGCCTTTACTGGTTCTCTCTGGTTAGACCAGATCTGAGCCTGGG
+>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1
+GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCACCTCCCAACCC
+>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1
+CAGAGGAGGTCTCTCGACGCAGGACTCGGCTTGCTGAAGGGCGCACGGCAAGAGGCGAGGGGCGGCGACT
+>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1
+GTCTGGGGCATCAAGCAGCTCCAGGCAAGAATGCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCC
+>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1
+TTTTTCAGTTCGCTTAGATGAAGACTTCAGGCAGTATACTGCATTTACCATACCTAGTATAAACAATGAG
+>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1
+ACAGCGACGAAGAGCTCATCAGAACAGACAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTATTACAT
+>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1
+TATCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATCCTAGGAAAATGTCTAACAGC
+>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1
+GGGGGGAACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAA
+>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1
+GTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACAT
+>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1
+TGCTCTGAAGAAAATTCCCTGGCCTTCCCTTGTAGTAAGGCCATATCTTCCCTAAAAAATTAGCCTGTCT
+>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1
+GGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATGTACCACCCACAAGGCTACTTCCC
+>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1
+TGATTTGTTGTGTCAGTTAGGGTGACAACTTTTTGTGTTCCTCTATTAGTAACATATCCTGCTTTTCCTA
+>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1
+TAACGCCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAACAAGCCCCAGAAGACGAAGGG
+>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1
+GTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCT
+>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1
+TTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGG
+>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1
+CTCTAGTGTCCATTCATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTCCATCTCTCCT
+>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1
+AGCCATTGCTCTCCAATTACTGTGATATTTCTCATGTTCATCTTGGGCCTTAACTATTCCATCTAAAAAT
+>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1
+TGCTGCTGGCTCAGCTCGTCTCATTCATTCCCTTACAGTAGGCCATCCAATCACACTACATATTGACCAC
+>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1
+TCGGAGTCATTGTTGCTATTACCACCATCTTTTGTTCATAGCAGCCCTGTAATATTTGATTAACATCTAA
+>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1
+ATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACAT
+>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1
+TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCCTCATCCTGTCTCCTTGCCACACAATCATCACCTG
+>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1
+ACCCATCTTATAGCAAAATCCTTTCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGAATAGCTCTACA
+>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1
+GAGGGGGAGTTGTTGTCTGTACCCCAGACCTGAAGCTCTCTTCTTGTGGGGCTGTTGGCTCTGGTCTGCT
+>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1
+TATAAAGACGCAGAAGTTATTCCAGCATACACAGGGCAGGAAACAGCATATTTTCTTTTCAAATTAGCAG
+>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1
+TCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGACTCTGTCTCTCTC
+>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1
+TGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTG
+>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1
+GGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAACAGTAGTGCGAAGAAGAAAAGCAAA
+>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1
+AAGTGCAAGCAATCTGATTCACCCGATTTCTTCCAATTATGATGACAGGTGTAGGTCCTACTAATACAGT
+>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1
+TATGGTACCAGTTAGAGAAAGAACCCCTAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAG
+>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1
+ATTGTACACATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGA
+>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1
+TTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAA
+>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1
+TGACAGAAACCTAGTTGGTCCAAAATGCGAACCCAGATTGTAAGACAATTTTAAAAGCATTGGGACCAGC
+>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1
+GGTGATATGGGCTGATGTACCATTTGCCCCTGGATGTTCTGCACTATAGGGTAATTTTGGCTGACCTGAT
+>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1
+GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATC
+>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1
+GCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCACCTAGCAATTCA
+>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1
+GGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCG
+>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1
+TCCTGACTCCAATACTGTAGGAGATTCCACCAATATTTGAGGGCTTCCCACCCCCTGCGTCCCAGAAGTT
+>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1
+ATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGATGAC
+>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1
+CAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGAGTGGTCCA
+>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1
+CACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATC
+>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1
+CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAGTTAGCCAGAGAGCTCCCA
+>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1
+ACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCCG
+>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1
+AATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAAT
+>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1
+TTAAAATTTTCTGTCACATTTACCAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACACAGGCATGTG
+>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1
+TCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGCATAGCTCTACAAGCTCCTTGTACTACTTCAATAA
+>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1
+TGTGTTCAGCTGTACTATTATGGTTATAGCATTTTCCGTGAAATTGACAGATCTAATTACTACCTCTTCT
+>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1
+GATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAAAAAGTTCAGAAGTACACATCCCACTAGG
+>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1
+TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCCAATTCTGAAACTGGATAAACAGCAGTTGTT
+>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1
+AGTTCATGTATCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGGCTGAAACAGCATAT
+>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1
+GGAGCTAGAACGATTCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGA
+>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1
+AAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTA
+>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1
+AGTAAGTAGTACCTGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCACTAATAAT
+>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1
+CGAGCAAGCTTCACAGGAGTTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGAT
+>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1
+GACCAGCAAAGCACCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGT
+>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1
+CCCCATATTACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTACATCATTAGTGT
+>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1
+TCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTA
+>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1
+TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTGCCAAAGAAGACAAGATATCCTTGATCTGAGGA
+>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1
+ACAGTAGAAAAATTCCCCTCCACAATTAAAACTGTGGTTACAATTTCTGGGTCCCCTCCTGAGGATTGCT
+>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1
+CGGGCACACACTACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTCCCTAGTTAGC
+>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1
+TTCTGAGGGGGAGATGTTGTCTCTAGCCCAGACCTGAAGCTCTCTTCTGGTGGGGCAGTTGGCTCTGGTC
+>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1
+ATGTATGGGAATTGGCTGAAAGGATACCTTTGGACAGGCCTGAGTAATGACTGAGGTGTTACAACTTGTC
+>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1
+CACCCATCCAAAGGAATTGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCCACCTCGACAG
+>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1
+TGCTAATTTTAAAAGACAATATTCTGTTTCCTGCCCTGTTTCTGCTGGAATAACTTCTGCTTCTATATAT
+>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1
+TTTTATGGTTCATAATCCACTCCATGTACTGGTTCTTTTAGAATCTCTCATTTTTCTGCCCGTTCTAGCT
+>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1
+CTTTATATTTTTTCTTACCCCCTGGCCTTAACCGAATTTTTTCCCATCGATCTAATTCTCCCCCGCTTAA
+>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1
+TAGGAACCAAAGAAAGATAGTTAAGTGTTTCAATTGTGGCACAGAAGGGCACACAGCCAGAAATTGCAGG
+>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1
+TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGGCTATACATTC
+>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1
+ATAGAGCTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGGGACGTTGCCAAAGAGTGACCTGAGG
+>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1
+GAAGTCTTGAGTTCTCTTATTAAGTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTC
+>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1
+TTTGATTGACTAACTCTGATTCACTTTGATCTTGTAGTGCTTGAATGATTCCTAATGCATATTGTGAGTC
+>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1
+ACTTTATATTTATATAATTCACTTCTCCAATTGTCCCTCATCTCTCCTCCTCCAGGTCTGAAGATCTCGG
+>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1
+AGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGTAGCCAGTAGATCCTAGACTATAGCCCTGG
+>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1
+GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACCAGTACATGGAGTGTATTATGACC
+>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1
+CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATAATTGCCTTAC
+>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1
+AAGCTTGTGTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATTCCAACTCTGTTCCAGAG
+>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1
+TCCCTGTTCGGGCGCCACTGCTAGAGATTTTCCACACTGACTAAAAGGGTCTGAGGGATCTCTAGTTACC
+>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1
+GCCACAGAGGGAGCCACACAATGAATGGACACTATAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGA
+>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1
+CAGATACCTAAATGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCCCTGCT
+>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1
+AATAGTACTTTCCTGATTCCAGCACTGACTAAATTATCTACTTGTTCATTTCCTCCAATTCCTTTGTGTG
+>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1
+AATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGCAGGAAGCAACCACCACTCTATTTTGTGCATC