# HG changeset patch
# User iuc
# Date 1563385331 14400
# Node ID ccebde0e2d6193429f2fe25985b581a0becd0eba

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a

diff -r 000000000000 -r ccebde0e2d61 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Jul 17 13:42:11 2019 -0400
@@ -0,0 +1,17 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@VERSION@">1.0.4</token>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @UNPUBLISHED{spond,
+                    author = "Sergei Kosakovsky Pond",
+                    title = "HyPhy: Hypothesis Testing using Phylogenies",
+                    year = "2000",
+                    note = "http://hyphy.org/",
+                    url = "http://hyphy.org/"}
+            </citation>
+            <yield />
+        </citations>
+    </xml>
+</macros>
\ No newline at end of file
diff -r 000000000000 -r ccebde0e2d61 test-data/readreduce-in1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/readreduce-in1.fa	Wed Jul 17 13:42:11 2019 -0400
@@ -0,0 +1,224 @@
+>B_FR_83_HXB2_ACC_K03455_5
+CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATT
+GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCA
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA
+AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACC
+AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC
+AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGC
+AAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTA
+GAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG
+CTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC
+AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAA
+ACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGG
+GAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+TAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA
+TAGTAGGAGCAGAAACCTTC
+>B_US_83_RF_ACC_M17451
+CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAGGAAAAAATAAAAGCAT
+TGGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCCAAAATT
+GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAGTTAGGAATACCACATCCTGCAGGGTTA
+AAAAAGAAGAAATCAGTAACAGTATTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATAAAGAGTTCAGGAAGTATACTGCATTTACCATACCTA
+GTATAAACAATGAAACACCACGGATTAGATATCAGTACAATGTGCTTCCA
+CAAGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGTATGACAAAAAT
+CTTAGAGCCTTTTAAAAAACAAAATCCAGAAATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCATAGAATA
+AAAATAGAGGAACTGAGAGAACATCTGTTAAAGTGGGGGTTTACCACACC
+GGACAAGAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC
+AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC
+AAGTCAGATTTATGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAGTACAACTAACAAAAGAAGCAGAG
+CTAGAACTGGCAGAAAATAGGGAGATTCTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC
+AAGGCCAATGGACATACCAAATTTATCAAGAGCCATTTAAAAACCTGAAA
+ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTACAAAAAGTAGCCACAGAAAGCATAGTAATATGGG
+GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAGGCA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+CAATACCCCTCCCTTAGTAAAATTGTGGTACCAGTTAGAAAAAGAACCCA
+TAATAGGAGCAGAAACTTTC
+>B_US_86_JRFL_ACC_U63632
+CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTCAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATT
+GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAAAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA
+AAAAAGAGAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATAAAGACTTCAGGAAATATACTGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGGTATCAGTACAATGTGCTTCCG
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAATTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAGCA
+AAAATAGAGGAATTGAGACAACATCTGTTGAGGTGGGGGTTTACCACACC
+AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC
+TCCATCCTGACAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC
+AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTAAATTGGGC
+AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG
+CTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAGCCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAGCAGGGGC
+AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAATTCTGAAA
+ACAGGAAAATATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAAAAAATAGCCAATGAAAGCATAGTAATATGGG
+GAAAGATTCCTAAATTTAAATTACCCATACAAAAAGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+CAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA
+TAGTAGGAGCAGAAACTTTC
+>B_US_90_WEAU160_ACC_U21135
+CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAGAAAATAAAAGCAT
+TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATT
+GGGCCTGAAAATCCATATAATACTCCAGTATTTGCCATAAAGAAAAAAGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCTTCAGGGTTA
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTACCCTTAGATGAAGACTTCAGGAAGTACACTGCATTTACCATACCTA
+GTATAAACAATGAAACACCAGGGATTAGATATCAGTACAATGTGCTTCCA
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+ATTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA
+AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGATTTACCACACC
+AGACAAAAAACATCAAAAAGACCCTCCATTCCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAAAGCTGCCAGAAAAAGAA
+AGTTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC
+AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAACTATGTAAACTCCTTA
+GGGGGACCAAAGCACTAACAGAAATAATACCAATAACAGAAGAAGCAGAG
+CTAGAGCTGGCAGAAAACAGGGAAATTCTAAAAGAACCGGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAGCTACAGAAGCAGGGGC
+AAGGCCAATGGACATATCAGATTTATCAAGAGCCATTTAAAAATCTGAAA
+ACAGGAAAGTATGCAAGAGTGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAGAAAATAACCACAGAAAGCATAGTAATATGGG
+GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+CAATACCCCTCCCTTAGTGAAATTATGGTATCAGTTAGAGAAAGAACCCA
+TAGTAGGAGCAGAAACTTTC
+>D_CD_83_ELI_ACC_K03454_7
+CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAACAGAAATTTGTACAGATATGGAAAAGGAAGGAAAAATTTCAAGAATT
+GGGCCTGAAAATCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA
+CAGTACCAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGATTTCTGGGAAGTTCAATTAGGAATACCGCATCCTGCAGGGCTG
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATGAAGATTTTAGGAAATATACCGCCTTTACCATATCTA
+GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCA
+CAGGGATGGAAAGGATCACCGGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCCTTTAGAAAACAAAATCCAGAAATGGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGGACA
+AAAATAGAGAAATTAAGAGAACATCTATTGAGGTGGGGATTTACCAGACC
+AGATAAAAAACATCAGAAAGAACCCCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGTCTATAAAACTGCCAGAAAAGGAG
+AGCTGGACTGTCAATGATATACAGAACTTAGTGGAGAGATTAAACTGGGC
+AAGCCAGATTTATCCAGGAATTAAAGTAAGACAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAA
+TTAGAACTGGCAGAAAACAGGGAAATTTTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAAGGGC
+ACGGCCAATGGACATACCAAATTTATCAAGAACCATTTAAAAATCTGAAA
+ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAGCA
+ATTAGCAGAGGCAGTGCAAAGAATATCCACAGAAAGCATAGTGATATGGG
+GAAGGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA
+TGGTGGGCAGAGTATTGGCAAGCCACTTGGATTCCTGAGTGGGAATTTGT
+CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA
+TAATAGGAGCAGAAACTTTC
+>D_CD_83_NDK_ACC_M27323
+CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAACAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAGAATT
+GGGCCTGAAAATCCATATAATACTCCAATATTTGCCATAAAGAAAAAAGA
+CAGTACCAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGATTTCTGGGAGGTTCAATTAGGAATACCGCATCCTGCAGGGCTG
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTCTC
+AGTTCCCTTAGATGAAGATTTTAGGAAATATACCGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTCCCA
+CAGGGATGGAAAGGATCACCGGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCCTTTAGAAAACAAAATCCAGAAATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA
+AAAATAGAGGAATTAAGAGAACATCTATTGAGGTGGGGATTTACCACACC
+AGATAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAAACCTGCCAGAAAAAGAA
+AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGGAAATTAAACTGGGC
+AAGCCAGATTTATGCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAGTACCACTAACAGAAGAAGCAGAA
+TTAGAACTGGCAGAAAACAGGGAAATTCTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAACAAGGGG
+ACGGCCAATGGACATACCAAATTTATCAAGAACCATTTAAAAATCTAAAA
+ACAGGAAAGTATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAAAAAATAGCCACAGAAAGCATAGTGATATGGG
+GAAAGACTCCTAAATTTAAACTACCCATACAAAAGGAAACATGGGAAACA
+TGGTGGATAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGT
+CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA
+TAATAGGAGCAGAAACTTTC
+>D_CD_84_84ZR085_ACC_U88822
+CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCAT
+TAACAGAAATTTGTACAGATATGGAAAAGGAAGGAAAAATTTCAAGAATT
+GGGCCTGAAAATCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA
+CAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGGATACCACATCCTGCAGGATTA
+AAGAAGAAAAAGTCAATAACAGTACTGGATGTGGGCGATGCATATTTTTC
+AATTCCCTTATGTGAAGACTTTAGGAAGTACACTGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTACTTCCA
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGATAAAAAT
+CTTAGAGCCCTTTAGAAAACAAAATCCAGAAGTAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGACAGCATAGAGCA
+AAAATAGAGAAATTAAGAGAACATCTGTTGAGGTGGGGGCTTACCACACC
+AGACAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAGTGGACAGTACAGTCTATAACACTGCCAGAGAAAGAA
+AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGC
+AAGCCAGATTTATCCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAGGCACTAACAGAGGTAATACCACTAACAGAAGAAGCAGAA
+TTAGAACTGGCAGAAAACAGGGAGATTCTAAAGGAACCAATGCATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAATTACAGAAACAAGGGC
+AAGGTCAATGGACATATCAAATTTATCAAGAACCATTTAAAAATCTGAAA
+ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA
+GTTAACAGAGGCAGTGCAAAAAATAGCCATAGAAAGCATAGTGATATGGG
+GAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA
+TGGTGGATAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGT
+CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA
+TAATAGGAGCAGAAACTTTC
+>D_UG_94_94UG114_ACC_U88824
+CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGGATGGA
+TGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCAC
+TAATAGAAATTTGTTCAGAACTAGAAAAGGAAGGAAAAATTTCAAAAATT
+GGGCCTGAAAACCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA
+CAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTTTGGGAAGTTCAACTAGGAATACCACATCCTGCAGGGCTA
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGACGCATATTTTTC
+AGTTCCCTTACATGAAGACTTTAGAAAATATACCGCATTCACCATACCTA
+GTACAAACAATGAGACACCAGGAATTAGATATCAGTACAATGTGCTTCCA
+CAAGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAACCTTTTAGAAAACAAAATCCAGAAATGATTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAATA
+AAAATAGAGGAATTAAGGGGACACCTCTTGAAGTGGGGATTTACCACACC
+AGACAAAAAGTATCAGAAAGAACCCCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAGTGGACAGTACAGCCTATACATCTGCCAGAAAAGGAA
+AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGC
+AAGCCAGATTTATCCAGGAATTAAAGTAAGACAATTATGCAAATGCCTTA
+GGGGAGCCAAAGCACTGACAGAAGTAATACCACTGACAGCAGAAGCAGAA
+TTAGAACTGGCAGAAAACAGGGAAATACTAAAAGAACCAGTACATGGAGC
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAAGGGC
+AAGATCAATGGACATATCAAATATATCAAGAACAATATAAAAATCTGAAA
+ACAGGAAAGTATGCGAAAATGAGGGGTACCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAGAAAATAGCCCAAGAATGTATAGTAATATGGG
+GAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAGGCCACCTGGATTCCTGAGTGGGAGTATGT
+CAACACCCCTCCTTTAGTTAAATTATGGTATCAGTTAGAGAAGGAACCCA
+TAGTAGGAGCAGAAACTTTC
diff -r 000000000000 -r ccebde0e2d61 test-data/readreduce-in2.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/readreduce-in2.fa	Wed Jul 17 13:42:11 2019 -0400
@@ -0,0 +1,112 @@
+>B_FR_83_HXB2_ACC_K03455_5
+CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATT
+GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCA
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA
+AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACC
+AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC
+AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGC
+AAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTA
+GAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG
+CTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC
+AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAA
+ACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGG
+GAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+TAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA
+TAGTAGGAGCAGAAACCTTC
+>B_US_83_RF_ACC_M17451
+CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAGGAAAAAATAAAAGCAT
+TGGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCCAAAATT
+GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAGTTAGGAATACCACATCCTGCAGGGTTA
+AAAAAGAAGAAATCAGTAACAGTATTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATAAAGAGTTCAGGAAGTATACTGCATTTACCATACCTA
+GTATAAACAATGAAACACCACGGATTAGATATCAGTACAATGTGCTTCCA
+CAAGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGTATGACAAAAAT
+CTTAGAGCCTTTTAAAAAACAAAATCCAGAAATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCATAGAATA
+AAAATAGAGGAACTGAGAGAACATCTGTTAAAGTGGGGGTTTACCACACC
+GGACAAGAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC
+AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC
+AAGTCAGATTTATGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAGTACAACTAACAAAAGAAGCAGAG
+CTAGAACTGGCAGAAAATAGGGAGATTCTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC
+AAGGCCAATGGACATACCAAATTTATCAAGAGCCATTTAAAAACCTGAAA
+ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTACAAAAAGTAGCCACAGAAAGCATAGTAATATGGG
+GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAGGCA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+CAATACCCCTCCCTTAGTAAAATTGTGGTACCAGTTAGAAAAAGAACCCA
+TAATAGGAGCAGAAACTTTC
+>B_US_86_JRFL_ACC_U63632
+CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTCAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATT
+GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAAAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA
+AAAAAGAGAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATAAAGACTTCAGGAAATATACTGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGGTATCAGTACAATGTGCTTCCG
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAATTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAGCA
+AAAATAGAGGAATTGAGACAACATCTGTTGAGGTGGGGGTTTACCACACC
+AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC
+TCCATCCTGACAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC
+AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTAAATTGGGC
+AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG
+CTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAGCCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAGCAGGGGC
+AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAATTCTGAAA
+ACAGGAAAATATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAAAAAATAGCCAATGAAAGCATAGTAATATGGG
+GAAAGATTCCTAAATTTAAATTACCCATACAAAAAGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+CAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA
+TAGTAGGAGCAGAAACTTTC
+>B_US_90_WEAU160_ACC_U21135
+CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAGAAAATAAAAGCAT
+TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATT
+GGGCCTGAAAATCCATATAATACTCCAGTATTTGCCATAAAGAAAAAAGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCTTCAGGGTTA
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTACCCTTAGATGAAGACTTCAGGAAGTACACTGCATTTACCATACCTA
+GTATAAACAATGAAACACCAGGGATTAGATATCAGTACAATGTGCTTCCA
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+ATTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA
+AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGATTTACCACACC
+AGACAAAAAACATCAAAAAGACCCTCCATTCCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAAAGCTGCCAGAAAAAGAA
+AGTTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC
+AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAACTATGTAAACTCCTTA
+GGGGGACCAAAGCACTAACAGAAATAATACCAATAACAGAAGAAGCAGAG
+CTAGAGCTGGCAGAAAACAGGGAAATTCTAAAAGAACCGGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAGCTACAGAAGCAGGGGC
+AAGGCCAATGGACATATCAGATTTATCAAGAGCCATTTAAAAATCTGAAA
+ACAGGAAAGTATGCAAGAGTGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAGAAAATAACCACAGAAAGCATAGTAATATGGG
+GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+CAATACCCCTCCCTTAGTGAAATTATGGTATCAGTTAGAGAAAGAACCCA
+TAGTAGGAGCAGAAACTTTC
\ No newline at end of file
diff -r 000000000000 -r ccebde0e2d61 test-data/readreduce-out1.fa
diff -r 000000000000 -r ccebde0e2d61 test-data/readreduce-out2.fa
diff -r 000000000000 -r ccebde0e2d61 test-data/tn93-in1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tn93-in1.fa	Wed Jul 17 13:42:11 2019 -0400
@@ -0,0 +1,224 @@
+>B_FR_83_HXB2_ACC_K03455_5
+CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATT
+GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCA
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA
+AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACC
+AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC
+AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGC
+AAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTA
+GAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG
+CTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC
+AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAA
+ACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGG
+GAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+TAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA
+TAGTAGGAGCAGAAACCTTC
+>B_US_83_RF_ACC_M17451
+CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAGGAAAAAATAAAAGCAT
+TGGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCCAAAATT
+GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAGTTAGGAATACCACATCCTGCAGGGTTA
+AAAAAGAAGAAATCAGTAACAGTATTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATAAAGAGTTCAGGAAGTATACTGCATTTACCATACCTA
+GTATAAACAATGAAACACCACGGATTAGATATCAGTACAATGTGCTTCCA
+CAAGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGTATGACAAAAAT
+CTTAGAGCCTTTTAAAAAACAAAATCCAGAAATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCATAGAATA
+AAAATAGAGGAACTGAGAGAACATCTGTTAAAGTGGGGGTTTACCACACC
+GGACAAGAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC
+AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC
+AAGTCAGATTTATGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAGTACAACTAACAAAAGAAGCAGAG
+CTAGAACTGGCAGAAAATAGGGAGATTCTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC
+AAGGCCAATGGACATACCAAATTTATCAAGAGCCATTTAAAAACCTGAAA
+ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTACAAAAAGTAGCCACAGAAAGCATAGTAATATGGG
+GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAGGCA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+CAATACCCCTCCCTTAGTAAAATTGTGGTACCAGTTAGAAAAAGAACCCA
+TAATAGGAGCAGAAACTTTC
+>B_US_86_JRFL_ACC_U63632
+CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTCAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATT
+GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAAAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA
+AAAAAGAGAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATAAAGACTTCAGGAAATATACTGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGGTATCAGTACAATGTGCTTCCG
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAATTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAGCA
+AAAATAGAGGAATTGAGACAACATCTGTTGAGGTGGGGGTTTACCACACC
+AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC
+TCCATCCTGACAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC
+AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTAAATTGGGC
+AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG
+CTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAGCCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAGCAGGGGC
+AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAATTCTGAAA
+ACAGGAAAATATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAAAAAATAGCCAATGAAAGCATAGTAATATGGG
+GAAAGATTCCTAAATTTAAATTACCCATACAAAAAGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+CAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA
+TAGTAGGAGCAGAAACTTTC
+>B_US_90_WEAU160_ACC_U21135
+CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAGAAAATAAAAGCAT
+TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATT
+GGGCCTGAAAATCCATATAATACTCCAGTATTTGCCATAAAGAAAAAAGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCTTCAGGGTTA
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTACCCTTAGATGAAGACTTCAGGAAGTACACTGCATTTACCATACCTA
+GTATAAACAATGAAACACCAGGGATTAGATATCAGTACAATGTGCTTCCA
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+ATTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA
+AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGATTTACCACACC
+AGACAAAAAACATCAAAAAGACCCTCCATTCCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAAAGCTGCCAGAAAAAGAA
+AGTTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC
+AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAACTATGTAAACTCCTTA
+GGGGGACCAAAGCACTAACAGAAATAATACCAATAACAGAAGAAGCAGAG
+CTAGAGCTGGCAGAAAACAGGGAAATTCTAAAAGAACCGGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAGCTACAGAAGCAGGGGC
+AAGGCCAATGGACATATCAGATTTATCAAGAGCCATTTAAAAATCTGAAA
+ACAGGAAAGTATGCAAGAGTGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAGAAAATAACCACAGAAAGCATAGTAATATGGG
+GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+CAATACCCCTCCCTTAGTGAAATTATGGTATCAGTTAGAGAAAGAACCCA
+TAGTAGGAGCAGAAACTTTC
+>D_CD_83_ELI_ACC_K03454_7
+CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAACAGAAATTTGTACAGATATGGAAAAGGAAGGAAAAATTTCAAGAATT
+GGGCCTGAAAATCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA
+CAGTACCAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGATTTCTGGGAAGTTCAATTAGGAATACCGCATCCTGCAGGGCTG
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATGAAGATTTTAGGAAATATACCGCCTTTACCATATCTA
+GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCA
+CAGGGATGGAAAGGATCACCGGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCCTTTAGAAAACAAAATCCAGAAATGGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGGACA
+AAAATAGAGAAATTAAGAGAACATCTATTGAGGTGGGGATTTACCAGACC
+AGATAAAAAACATCAGAAAGAACCCCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGTCTATAAAACTGCCAGAAAAGGAG
+AGCTGGACTGTCAATGATATACAGAACTTAGTGGAGAGATTAAACTGGGC
+AAGCCAGATTTATCCAGGAATTAAAGTAAGACAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAA
+TTAGAACTGGCAGAAAACAGGGAAATTTTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAAGGGC
+ACGGCCAATGGACATACCAAATTTATCAAGAACCATTTAAAAATCTGAAA
+ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAGCA
+ATTAGCAGAGGCAGTGCAAAGAATATCCACAGAAAGCATAGTGATATGGG
+GAAGGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA
+TGGTGGGCAGAGTATTGGCAAGCCACTTGGATTCCTGAGTGGGAATTTGT
+CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA
+TAATAGGAGCAGAAACTTTC
+>D_CD_83_NDK_ACC_M27323
+CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAACAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAGAATT
+GGGCCTGAAAATCCATATAATACTCCAATATTTGCCATAAAGAAAAAAGA
+CAGTACCAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGATTTCTGGGAGGTTCAATTAGGAATACCGCATCCTGCAGGGCTG
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTCTC
+AGTTCCCTTAGATGAAGATTTTAGGAAATATACCGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTCCCA
+CAGGGATGGAAAGGATCACCGGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCCTTTAGAAAACAAAATCCAGAAATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA
+AAAATAGAGGAATTAAGAGAACATCTATTGAGGTGGGGATTTACCACACC
+AGATAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAAACCTGCCAGAAAAAGAA
+AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGGAAATTAAACTGGGC
+AAGCCAGATTTATGCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAGTACCACTAACAGAAGAAGCAGAA
+TTAGAACTGGCAGAAAACAGGGAAATTCTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAACAAGGGG
+ACGGCCAATGGACATACCAAATTTATCAAGAACCATTTAAAAATCTAAAA
+ACAGGAAAGTATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAAAAAATAGCCACAGAAAGCATAGTGATATGGG
+GAAAGACTCCTAAATTTAAACTACCCATACAAAAGGAAACATGGGAAACA
+TGGTGGATAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGT
+CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA
+TAATAGGAGCAGAAACTTTC
+>D_CD_84_84ZR085_ACC_U88822
+CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCAT
+TAACAGAAATTTGTACAGATATGGAAAAGGAAGGAAAAATTTCAAGAATT
+GGGCCTGAAAATCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA
+CAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGGATACCACATCCTGCAGGATTA
+AAGAAGAAAAAGTCAATAACAGTACTGGATGTGGGCGATGCATATTTTTC
+AATTCCCTTATGTGAAGACTTTAGGAAGTACACTGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTACTTCCA
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGATAAAAAT
+CTTAGAGCCCTTTAGAAAACAAAATCCAGAAGTAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGACAGCATAGAGCA
+AAAATAGAGAAATTAAGAGAACATCTGTTGAGGTGGGGGCTTACCACACC
+AGACAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAGTGGACAGTACAGTCTATAACACTGCCAGAGAAAGAA
+AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGC
+AAGCCAGATTTATCCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAGGCACTAACAGAGGTAATACCACTAACAGAAGAAGCAGAA
+TTAGAACTGGCAGAAAACAGGGAGATTCTAAAGGAACCAATGCATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAATTACAGAAACAAGGGC
+AAGGTCAATGGACATATCAAATTTATCAAGAACCATTTAAAAATCTGAAA
+ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA
+GTTAACAGAGGCAGTGCAAAAAATAGCCATAGAAAGCATAGTGATATGGG
+GAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA
+TGGTGGATAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGT
+CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA
+TAATAGGAGCAGAAACTTTC
+>D_UG_94_94UG114_ACC_U88824
+CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGGATGGA
+TGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCAC
+TAATAGAAATTTGTTCAGAACTAGAAAAGGAAGGAAAAATTTCAAAAATT
+GGGCCTGAAAACCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA
+CAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTTTGGGAAGTTCAACTAGGAATACCACATCCTGCAGGGCTA
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGACGCATATTTTTC
+AGTTCCCTTACATGAAGACTTTAGAAAATATACCGCATTCACCATACCTA
+GTACAAACAATGAGACACCAGGAATTAGATATCAGTACAATGTGCTTCCA
+CAAGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAACCTTTTAGAAAACAAAATCCAGAAATGATTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAATA
+AAAATAGAGGAATTAAGGGGACACCTCTTGAAGTGGGGATTTACCACACC
+AGACAAAAAGTATCAGAAAGAACCCCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAGTGGACAGTACAGCCTATACATCTGCCAGAAAAGGAA
+AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGC
+AAGCCAGATTTATCCAGGAATTAAAGTAAGACAATTATGCAAATGCCTTA
+GGGGAGCCAAAGCACTGACAGAAGTAATACCACTGACAGCAGAAGCAGAA
+TTAGAACTGGCAGAAAACAGGGAAATACTAAAAGAACCAGTACATGGAGC
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAAGGGC
+AAGATCAATGGACATATCAAATATATCAAGAACAATATAAAAATCTGAAA
+ACAGGAAAGTATGCGAAAATGAGGGGTACCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAGAAAATAGCCCAAGAATGTATAGTAATATGGG
+GAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAGGCCACCTGGATTCCTGAGTGGGAGTATGT
+CAACACCCCTCCTTTAGTTAAATTATGGTATCAGTTAGAGAAGGAACCCA
+TAGTAGGAGCAGAAACTTTC
diff -r 000000000000 -r ccebde0e2d61 test-data/tn93-in2-alpha.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tn93-in2-alpha.fa	Wed Jul 17 13:42:11 2019 -0400
@@ -0,0 +1,112 @@
+>B_FR_83_HXB2_ACC_K03455_5
+CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATT
+GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCA
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA
+AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACC
+AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC
+AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGC
+AAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTA
+GAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG
+CTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC
+AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAA
+ACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGG
+GAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+TAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA
+TAGTAGGAGCAGAAACCTTC
+>B_US_83_RF_ACC_M17451
+CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAGGAAAAAATAAAAGCAT
+TGGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCCAAAATT
+GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAGTTAGGAATACCACATCCTGCAGGGTTA
+AAAAAGAAGAAATCAGTAACAGTATTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATAAAGAGTTCAGGAAGTATACTGCATTTACCATACCTA
+GTATAAACAATGAAACACCACGGATTAGATATCAGTACAATGTGCTTCCA
+CAAGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGTATGACAAAAAT
+CTTAGAGCCTTTTAAAAAACAAAATCCAGAAATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCATAGAATA
+AAAATAGAGGAACTGAGAGAACATCTGTTAAAGTGGGGGTTTACCACACC
+GGACAAGAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC
+AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC
+AAGTCAGATTTATGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAGTACAACTAACAAAAGAAGCAGAG
+CTAGAACTGGCAGAAAATAGGGAGATTCTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGC
+AAGGCCAATGGACATACCAAATTTATCAAGAGCCATTTAAAAACCTGAAA
+ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTACAAAAAGTAGCCACAGAAAGCATAGTAATATGGG
+GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAGGCA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+CAATACCCCTCCCTTAGTAAAATTGTGGTACCAGTTAGAAAAAGAACCCA
+TAATAGGAGCAGAAACTTTC
+>B_US_86_JRFL_ACC_U63632
+CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTCAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATT
+GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAAAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTA
+AAAAAGAGAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATAAAGACTTCAGGAAATATACTGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGGTATCAGTACAATGTGCTTCCG
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCTTTTAGAAAACAAAATCCAGACATAATTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAGCA
+AAAATAGAGGAATTGAGACAACATCTGTTGAGGTGGGGGTTTACCACACC
+AGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAAC
+TCCATCCTGACAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAC
+AGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTAAATTGGGC
+AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG
+CTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAGCCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAGCAGGGGC
+AAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAATTCTGAAA
+ACAGGAAAATATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAAAAAATAGCCAATGAAAGCATAGTAATATGGG
+GAAAGATTCCTAAATTTAAATTACCCATACAAAAAGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+CAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCA
+TAGTAGGAGCAGAAACTTTC
+>B_US_90_WEAU160_ACC_U21135
+CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAGAAAATAAAAGCAT
+TAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATT
+GGGCCTGAAAATCCATATAATACTCCAGTATTTGCCATAAAGAAAAAAGA
+CAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCTTCAGGGTTA
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTACCCTTAGATGAAGACTTCAGGAAGTACACTGCATTTACCATACCTA
+GTATAAACAATGAAACACCAGGGATTAGATATCAGTACAATGTGCTTCCA
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+ATTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA
+AAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGATTTACCACACC
+AGACAAAAAACATCAAAAAGACCCTCCATTCCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAAAGCTGCCAGAAAAAGAA
+AGTTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGC
+AAGTCAGATTTACGCAGGGATTAAAGTAAAGCAACTATGTAAACTCCTTA
+GGGGGACCAAAGCACTAACAGAAATAATACCAATAACAGAAGAAGCAGAG
+CTAGAGCTGGCAGAAAACAGGGAAATTCTAAAAGAACCGGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAGCTACAGAAGCAGGGGC
+AAGGCCAATGGACATATCAGATTTATCAAGAGCCATTTAAAAATCTGAAA
+ACAGGAAAGTATGCAAGAGTGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAGAAAATAACCACAGAAAGCATAGTAATATGGG
+GAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGT
+CAATACCCCTCCCTTAGTGAAATTATGGTATCAGTTAGAGAAAGAACCCA
+TAGTAGGAGCAGAAACTTTC
\ No newline at end of file
diff -r 000000000000 -r ccebde0e2d61 test-data/tn93-in2-beta.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tn93-in2-beta.fa	Wed Jul 17 13:42:11 2019 -0400
@@ -0,0 +1,112 @@
+>D_CD_83_ELI_ACC_K03454_7
+CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAACAGAAATTTGTACAGATATGGAAAAGGAAGGAAAAATTTCAAGAATT
+GGGCCTGAAAATCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA
+CAGTACCAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGATTTCTGGGAAGTTCAATTAGGAATACCGCATCCTGCAGGGCTG
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTC
+AGTTCCCTTAGATGAAGATTTTAGGAAATATACCGCCTTTACCATATCTA
+GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCA
+CAGGGATGGAAAGGATCACCGGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCCTTTAGAAAACAAAATCCAGAAATGGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGGACA
+AAAATAGAGAAATTAAGAGAACATCTATTGAGGTGGGGATTTACCAGACC
+AGATAAAAAACATCAGAAAGAACCCCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGTCTATAAAACTGCCAGAAAAGGAG
+AGCTGGACTGTCAATGATATACAGAACTTAGTGGAGAGATTAAACTGGGC
+AAGCCAGATTTATCCAGGAATTAAAGTAAGACAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAA
+TTAGAACTGGCAGAAAACAGGGAAATTTTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAAGGGC
+ACGGCCAATGGACATACCAAATTTATCAAGAACCATTTAAAAATCTGAAA
+ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAGCA
+ATTAGCAGAGGCAGTGCAAAGAATATCCACAGAAAGCATAGTGATATGGG
+GAAGGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA
+TGGTGGGCAGAGTATTGGCAAGCCACTTGGATTCCTGAGTGGGAATTTGT
+CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA
+TAATAGGAGCAGAAACTTTC
+>D_CD_83_NDK_ACC_M27323
+CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCAT
+TAACAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAGAATT
+GGGCCTGAAAATCCATATAATACTCCAATATTTGCCATAAAGAAAAAAGA
+CAGTACCAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGATTTCTGGGAGGTTCAATTAGGAATACCGCATCCTGCAGGGCTG
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTCTC
+AGTTCCCTTAGATGAAGATTTTAGGAAATATACCGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTCCCA
+CAGGGATGGAAAGGATCACCGGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAGCCCTTTAGAAAACAAAATCCAGAAATAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACA
+AAAATAGAGGAATTAAGAGAACATCTATTGAGGTGGGGATTTACCACACC
+AGATAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAATGGACAGTACAGCCTATAAACCTGCCAGAAAAAGAA
+AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGGAAATTAAACTGGGC
+AAGCCAGATTTATGCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAAGCACTAACAGAAGTAGTACCACTAACAGAAGAAGCAGAA
+TTAGAACTGGCAGAAAACAGGGAAATTCTAAAAGAACCAGTACATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAACAAGGGG
+ACGGCCAATGGACATACCAAATTTATCAAGAACCATTTAAAAATCTAAAA
+ACAGGAAAGTATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAAAAAATAGCCACAGAAAGCATAGTGATATGGG
+GAAAGACTCCTAAATTTAAACTACCCATACAAAAGGAAACATGGGAAACA
+TGGTGGATAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGT
+CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA
+TAATAGGAGCAGAAACTTTC
+>D_CD_84_84ZR085_ACC_U88822
+CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGA
+TGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCAT
+TAACAGAAATTTGTACAGATATGGAAAAGGAAGGAAAAATTTCAAGAATT
+GGGCCTGAAAATCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA
+CAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTCTGGGAAGTTCAATTAGGGATACCACATCCTGCAGGATTA
+AAGAAGAAAAAGTCAATAACAGTACTGGATGTGGGCGATGCATATTTTTC
+AATTCCCTTATGTGAAGACTTTAGGAAGTACACTGCATTTACCATACCTA
+GTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTACTTCCA
+CAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGATAAAAAT
+CTTAGAGCCCTTTAGAAAACAAAATCCAGAAGTAGTTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGACAGCATAGAGCA
+AAAATAGAGAAATTAAGAGAACATCTGTTGAGGTGGGGGCTTACCACACC
+AGACAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAGTGGACAGTACAGTCTATAACACTGCCAGAGAAAGAA
+AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGC
+AAGCCAGATTTATCCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTA
+GGGGAACCAAGGCACTAACAGAGGTAATACCACTAACAGAAGAAGCAGAA
+TTAGAACTGGCAGAAAACAGGGAGATTCTAAAGGAACCAATGCATGGAGT
+GTATTATGACCCATCAAAAGACTTAATAGCAGAATTACAGAAACAAGGGC
+AAGGTCAATGGACATATCAAATTTATCAAGAACCATTTAAAAATCTGAAA
+ACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA
+GTTAACAGAGGCAGTGCAAAAAATAGCCATAGAAAGCATAGTGATATGGG
+GAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA
+TGGTGGATAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGT
+CAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCA
+TAATAGGAGCAGAAACTTTC
+>D_UG_94_94UG114_ACC_U88824
+CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGGATGGA
+TGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCAC
+TAATAGAAATTTGTTCAGAACTAGAAAAGGAAGGAAAAATTTCAAAAATT
+GGGCCTGAAAACCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGA
+CAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAA
+CTCAAGACTTTTGGGAAGTTCAACTAGGAATACCACATCCTGCAGGGCTA
+AAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGACGCATATTTTTC
+AGTTCCCTTACATGAAGACTTTAGAAAATATACCGCATTCACCATACCTA
+GTACAAACAATGAGACACCAGGAATTAGATATCAGTACAATGTGCTTCCA
+CAAGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAAT
+CTTAGAACCTTTTAGAAAACAAAATCCAGAAATGATTATCTATCAATACA
+TGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAATA
+AAAATAGAGGAATTAAGGGGACACCTCTTGAAGTGGGGATTTACCACACC
+AGACAAAAAGTATCAGAAAGAACCCCCATTTCTTTGGATGGGTTATGAAC
+TCCATCCTGATAAGTGGACAGTACAGCCTATACATCTGCCAGAAAAGGAA
+AGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGC
+AAGCCAGATTTATCCAGGAATTAAAGTAAGACAATTATGCAAATGCCTTA
+GGGGAGCCAAAGCACTGACAGAAGTAATACCACTGACAGCAGAAGCAGAA
+TTAGAACTGGCAGAAAACAGGGAAATACTAAAAGAACCAGTACATGGAGC
+GTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAAGGGC
+AAGATCAATGGACATATCAAATATATCAAGAACAATATAAAAATCTGAAA
+ACAGGAAAGTATGCGAAAATGAGGGGTACCCACACTAATGATGTAAAACA
+ATTAACAGAGGCAGTGCAGAAAATAGCCCAAGAATGTATAGTAATATGGG
+GAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACA
+TGGTGGACAGAGTATTGGCAGGCCACCTGGATTCCTGAGTGGGAGTATGT
+CAACACCCCTCCTTTAGTTAAATTATGGTATCAGTTAGAGAAGGAACCCA
+TAGTAGGAGCAGAAACTTTC
diff -r 000000000000 -r ccebde0e2d61 test-data/tn93-out1.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tn93-out1.csv	Wed Jul 17 13:42:11 2019 -0400
@@ -0,0 +1,29 @@
+B_FR_83_HXB2_ACC_K03455_5,B_US_83_RF_ACC_M17451,0.045156
+B_FR_83_HXB2_ACC_K03455_5,B_US_86_JRFL_ACC_U63632,0.0296218
+B_FR_83_HXB2_ACC_K03455_5,B_US_90_WEAU160_ACC_U21135,0.0327566
+B_FR_83_HXB2_ACC_K03455_5,D_CD_83_ELI_ACC_K03454_7,0.0669206
+B_FR_83_HXB2_ACC_K03455_5,D_CD_83_NDK_ACC_M27323,0.0592586
+B_FR_83_HXB2_ACC_K03455_5,D_CD_84_84ZR085_ACC_U88822,0.0663619
+B_FR_83_HXB2_ACC_K03455_5,D_UG_94_94UG114_ACC_U88824,0.0847988
+B_US_83_RF_ACC_M17451,B_US_86_JRFL_ACC_U63632,0.048328
+B_US_83_RF_ACC_M17451,B_US_90_WEAU160_ACC_U21135,0.0515908
+B_US_83_RF_ACC_M17451,D_CD_83_ELI_ACC_K03454_7,0.0810759
+B_US_83_RF_ACC_M17451,D_CD_83_NDK_ACC_M27323,0.0661066
+B_US_83_RF_ACC_M17451,D_CD_84_84ZR085_ACC_U88822,0.0769146
+B_US_83_RF_ACC_M17451,D_UG_94_94UG114_ACC_U88824,0.0955213
+B_US_86_JRFL_ACC_U63632,B_US_90_WEAU160_ACC_U21135,0.0408994
+B_US_86_JRFL_ACC_U63632,D_CD_83_ELI_ACC_K03454_7,0.0771797
+B_US_86_JRFL_ACC_U63632,D_CD_83_NDK_ACC_M27323,0.0609044
+B_US_86_JRFL_ACC_U63632,D_CD_84_84ZR085_ACC_U88822,0.0705011
+B_US_86_JRFL_ACC_U63632,D_UG_94_94UG114_ACC_U88824,0.0882054
+B_US_90_WEAU160_ACC_U21135,D_CD_83_ELI_ACC_K03454_7,0.0771856
+B_US_90_WEAU160_ACC_U21135,D_CD_83_NDK_ACC_M27323,0.0609097
+B_US_90_WEAU160_ACC_U21135,D_CD_84_84ZR085_ACC_U88822,0.0740203
+B_US_90_WEAU160_ACC_U21135,D_UG_94_94UG114_ACC_U88824,0.0890019
+D_CD_83_ELI_ACC_K03454_7,D_CD_83_NDK_ACC_M27323,0.0287246
+D_CD_83_ELI_ACC_K03454_7,D_CD_84_84ZR085_ACC_U88822,0.055948
+D_CD_83_ELI_ACC_K03454_7,D_UG_94_94UG114_ACC_U88824,0.0742033
+D_CD_83_NDK_ACC_M27323,D_CD_84_84ZR085_ACC_U88822,0.0491974
+D_CD_83_NDK_ACC_M27323,D_UG_94_94UG114_ACC_U88824,0.0726626
+D_CD_84_84ZR085_ACC_U88822,D_UG_94_94UG114_ACC_U88824,0.0805088
+ID1,ID2,Distance
diff -r 000000000000 -r ccebde0e2d61 test-data/tn93-out2.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tn93-out2.csv	Wed Jul 17 13:42:11 2019 -0400
@@ -0,0 +1,17 @@
+B_FR_83_HXB2_ACC_K03455_5,D_CD_83_ELI_ACC_K03454_7,0.0669206
+B_FR_83_HXB2_ACC_K03455_5,D_CD_83_NDK_ACC_M27323,0.0592586
+B_FR_83_HXB2_ACC_K03455_5,D_CD_84_84ZR085_ACC_U88822,0.0663619
+B_FR_83_HXB2_ACC_K03455_5,D_UG_94_94UG114_ACC_U88824,0.0847988
+B_US_83_RF_ACC_M17451,D_CD_83_ELI_ACC_K03454_7,0.0810759
+B_US_83_RF_ACC_M17451,D_CD_83_NDK_ACC_M27323,0.0661066
+B_US_83_RF_ACC_M17451,D_CD_84_84ZR085_ACC_U88822,0.0769146
+B_US_83_RF_ACC_M17451,D_UG_94_94UG114_ACC_U88824,0.0955213
+B_US_86_JRFL_ACC_U63632,D_CD_83_ELI_ACC_K03454_7,0.0771797
+B_US_86_JRFL_ACC_U63632,D_CD_83_NDK_ACC_M27323,0.0609044
+B_US_86_JRFL_ACC_U63632,D_CD_84_84ZR085_ACC_U88822,0.0705011
+B_US_86_JRFL_ACC_U63632,D_UG_94_94UG114_ACC_U88824,0.0882054
+B_US_90_WEAU160_ACC_U21135,D_CD_83_ELI_ACC_K03454_7,0.0771856
+B_US_90_WEAU160_ACC_U21135,D_CD_83_NDK_ACC_M27323,0.0609097
+B_US_90_WEAU160_ACC_U21135,D_CD_84_84ZR085_ACC_U88822,0.0740203
+B_US_90_WEAU160_ACC_U21135,D_UG_94_94UG114_ACC_U88824,0.0890019
+ID1,ID2,Distance
diff -r 000000000000 -r ccebde0e2d61 tn93.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tn93.xml	Wed Jul 17 13:42:11 2019 -0400
@@ -0,0 +1,95 @@
+<tool id="tn93" name="TN93" version="@VERSION@">
+    <description>compute distances between aligned sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">tn93</requirement>
+    </requirements>
+    <version_command><![CDATA[tn93 --version]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    tn93
+    -o '$tn93_distances'
+    #if str($options.advanced) == 'advanced':
+        -t $options.threshold
+        -a $options.ambigs
+        -g $options.fraction
+        -f csv
+        -l $options.overlap
+        #if $options.counts_in_name:
+            -d '$options.counts_in_name'
+        #end if
+    #end if
+    #if $second_fasta:
+        -s '$second_fasta'
+    #end if
+    '$input_fasta'
+    ]]></command>
+    <inputs>
+        <param name="input_fasta" type="data" format="fasta" label="Input in FASTA format" />
+        <param name="second_fasta" argument="-s" type="data" format="fasta" optional="true"
+            label="Additional input FASTA for pairwise comparisons" />
+        <conditional name="options">
+            <param label="Additional options" name="advanced" type="select">
+                <option value="defaults">Use defaults</option>
+                <option value="advanced">Specify additional parameters</option>
+            </param>
+            <when value="defaults" />
+            <when value="advanced">
+                <param name="threshold" type="float" value="0.015" label="Only report distances below this threshold" />
+                <param name="ambigs" argument="-a" type="select" label="Strategy for ambiguous nucleotides">
+                    <option value="handle">handle</option>
+                    <option value="resolve">resolve</option>
+                    <option value="average">average</option>
+                    <option value="skip">skip</option>
+                    <option value="gapmm">gapmm</option>
+                </param>
+                <param name="fraction" argument="-g" type="float" value="1.0"
+                    label="Maximum tolerated fraction of ambiguous characters" />
+                <param name="overlap" argument="-l" type="integer" value="100"
+                    label="Only count pairs that overlap by at least N bases" />
+                <param name="counts_in_name" argument="-d" type="text"
+                    optional="true" label="Sequence name component immediately preceding a copy number" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="csv" name="tn93_distances" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_fasta" value="tn93-in1.fa" />
+            <param name="advanced" value="advanced" />
+            <param name="threshold" value="0.35" />
+            <output file="tn93-out1.csv" ftype="csv" name="tn93_distances" sort="True" />
+        </test>
+        <test>
+            <param name="input_fasta" value="tn93-in2-alpha.fa" />
+            <param name="second_fasta" value="tn93-in2-beta.fa" />
+            <param name="advanced" value="advanced" />
+            <param name="threshold" value="0.35" />
+            <output file="tn93-out2.csv" ftype="csv" name="tn93_distances" sort="True" />
+        </test>
+    </tests>
+    <help><![CDATA[
+TN93
+----
+
+Compute pairwise distances between aligned
+nucleotide sequences in sequential FASTA format using the
+[Tamura Nei 93 distance](http://www.ncbi.nlm.nih.gov/pubmed/8336541).
+
+NOTES
+-----
+
+All sequences must be aligned and have the same length. Only IUPAC characters are recognized (e.g. no ~). Sequence names can include copy number as in
+
+  >seqname:10
+
+':' can be replaced with another character using `-d`, and sequences that have no explicit copy number are assumed to be a single copy. Copy numbers
+only affect histogram and mean calculations.
+]]></help>
+    <expand macro="citations">
+        <citation type="doi">10.1093/oxfordjournals.molbev.a040023</citation>
+    </expand>
+</tool>