# HG changeset patch
# User rnateam
# Date 1481891784 18000
# Node ID 8ad3e79255c1e44440a514c1908eea10e8a2e69d

planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053

diff -r 000000000000 -r 8ad3e79255c1 preMlocarna.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/preMlocarna.xml	Fri Dec 16 07:36:24 2016 -0500
@@ -0,0 +1,82 @@
+<tool id="preMloc" name="premlocarna" version="0.1.0" >
+	<requirements>
+		<requirement type="package" version="0.1">graphclust-wrappers</requirement>
+		<requirement type="package" version='0.1'>pgma-simple</requirement>
+	</requirements>
+	<stdio>
+		<exit_code range="1:" />
+	</stdio>
+	<command>
+		<![CDATA[
+
+		    'newpreMlocarna.pl'  $CI '$fast_cluster' '$fasta_data' '$fast_cluster_sim' '$data_map' $knn ''
+
+]]>
+	</command>
+	<inputs>
+		<param type="data" name="fast_cluster" label="fast_cluster" format="txt" help="stokholm format" />
+		<param type="data" name="fasta_data" label="fasta_data" format="fasta" help="fasta format" />
+		<param type="data" name="fast_cluster_sim" label="fast_cluster_sim" format="txt" help="similarity sclores" />
+		<param type="data" name="data_map" label="data_map" format="txt" help="data map" />
+		<param name="CI" type="integer" value="1" size="5" label="Number of current iteration "/>
+		<param name="knn" type="integer" value="20" size="5" label="Number of nearest neighbors" help="must be the same as for previous step"/>
+	</inputs>
+	<outputs>
+		<collection name="centers" type="list"  label="centers">
+			<discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.center.fa$)" ext="txt" directory="CLUSTER"  />
+		</collection>
+		<collection name="trees" type="list" label="trees">
+			<discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.tree$)"  ext="txt" directory="CLUSTER" />
+		</collection>
+		<collection name="cmFa" type="list"  label="cmfinder_fa" >
+			<discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.cmfinder.fa$)" ext="txt"  directory="CLUSTER" />
+		</collection>
+		<collection name="model_tree_fa" type="list"  label="model_tree_fa" >
+			<discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.model.tree.fa$)" ext="txt"  directory="CLUSTER" />
+		</collection>
+		<collection name="tree_matrix" type="list"  label="tree_matrix" >
+			<discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.matrix.tree$)" ext="txt"  directory="CLUSTER" />
+		</collection>
+	</outputs>
+	<tests>
+		<test>
+			<param name="fast_cluster" value="data.svector.1.fast_cluster"/>
+			<param name="fasta_data" value="data.fasta"/>
+			<param name="fast_cluster_sim" value="data.svector.1.fast_cluster_sim"/>
+			<param name="data_map" value="data.map"/>
+			<param name="knn" value="20"/>
+			<param name="CI" value="1"/>
+			<output_collection name="centers">
+				<element name="1.1.center.fa" file="CLUSTER/1.1.center.fa"/>
+				<element name="1.1.center.fa" file="CLUSTER/1.2.center.fa"/>
+			</output_collection>
+			<output_collection name="trees" >
+				<element name="1.1.tree" file="CLUSTER/1.1.tree"/>
+				<element name="1.2.tree" file="CLUSTER/1.2.tree"/>
+			</output_collection>
+			<output_collection name="cmFa">
+				<element name="1.1.cmfinder.fa" file="CLUSTER/1.1.cmfinder.fa"/>
+				<element name="1.2.cmfinder.fa" file="CLUSTER/1.2.cmfinder.fa"/>
+			</output_collection>
+			<output_collection name="tree_matrix">
+				<element name="1.1.matrix.tree" file="CLUSTER/1.1.matrix.tree"/>
+				<element name="1.2.matrix.tree" file="CLUSTER/1.2.matrix.tree"/>
+			</output_collection>
+		</test>
+	</tests>
+	<help>
+		<![CDATA[
+
+**What it does**
+
+This tool prepares files for locarna step.
+
+.. class:: warningmark
+
+The number of nearest neighbors must be the same as in the previous step (NSPDK step)
+
+]]>
+	</help>
+	<citations>
+  </citations>
+</tool>
diff -r 000000000000 -r 8ad3e79255c1 test-data/CLUSTER/1.1.center.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CLUSTER/1.1.center.fa	Fri Dec 16 07:36:24 2016 -0500
@@ -0,0 +1,40 @@
+>7 SEQ7#1#83#+ ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005_rep.12
+GUCAGGAUGGCCGAGCGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUCCCCUGGAGGCGUGGGUUCGAAUCCCACUUCUGACA
+>9 SEQ9#1#73#+ ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005_rep.14
+GCUUCUGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCAGAAGCA
+>10 SEQ10#1#73#+ ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005_rep.15
+GCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCG
+>15 SEQ15#1#73#+ ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005_rep.1
+GCCGAAAUAGCUCAGUUGGGAGAGCGUUAGACUGAAGAUCUAAAGGUCCCUGGUUCGAUCCCGGGUUUCGGCA
+>16 SEQ16#1#72#+ ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005_rep.20
+GGGGAUGUAGCUCAGUGGUAGAGCGCAUGCUUCGCAUGUAUGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCA
+>17 SEQ17#1#71#+ ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005_rep.21
+GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUCCCACGCGGGAGACCCGGGUUCAAUUCCCGGCCAAUGCA
+>18 SEQ18#1#72#+ ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005_rep.22
+GCGUUGGUGGUAUAGUGGUGAGCAUAGCUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCAACGCA
+>23 SEQ23#1#74#+ ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005_rep.27
+GGCCGGUUAGCUCAGUUGGUUAGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCA
+>28 SEQ28#1#71#+ ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005_rep.31
+GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUGCCACGCGGGAGGCCCGGGUUCGAUUCCCGGCCAAUGCA
+>30 SEQ30#1#72#+ ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005_rep.33
+GGCUCGUUGGUCUAGGGGUAUGAUUCUCGCUUAGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCC
+>31 SEQ31#1#73#+ ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005_rep.34
+GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCGGAAACA
+>32 SEQ32#1#73#+ ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005_rep.35
+GUUUCCGUAGUGUAGCGGUUAUCACAUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAUCCCGGGCGGAAACA
+>33 SEQ33#1#72#+ ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005_rep.36
+UCCUCGUUAGUAUAGUGGUGAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCGAUUCCCCGACGGGGAG
+>35 SEQ35#1#72#+ ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005_rep.38
+UCCCUGGUGGUCUAGUGGCUAGGAUUCGGCGCUUUCACCGCCGCGCCCCGGGUUCGAUUCCCGGCCAGGAAU
+>37 SEQ37#1#82#+ ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005_rep.3
+GGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGAUUUAGGCUCCAGUCUCUUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCA
+>46 SEQ46#1#72#+ ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005_rep.5
+UCCCUGGUGGUCUAGUGGUUAGGAUUCGGCGCUCUCACCGCCGCGGCCCGGGUUCGAUUCCCGGUCAGGGAA
+>51 SEQ51#1#88#+ ORIGID RF00006_rep.0_AF045145.1/1-88_51 ORIGHEAD RF00006_rep.0
+GGCUGGCUUUAGCUCAGCGGUUACUUCGCGUGUCAUCAAACCACCUCUCUGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGCCCUCUU
+>52 SEQ52#1#101#+ ORIGID RF00006_rep.1_AC005219.1/49914-50014_52 ORIGHEAD RF00006_rep.1
+GGGUCGGAGUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUGCUGGGGUUCGAGACCCGCGGGUGCUUACUGACCCUUUU
+>53 SEQ53#1#98#+ ORIGID RF00006_rep.2_AF045143.1/1-98_53 ORIGHEAD RF00006_rep.2
+GGCUGGCUUUAGCUCAGCGGUUACUUCGACAGUUCUUUAAUUGAAACAAGCAACCUGUCUGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGUCCUUUU
+>54 SEQ54#1#88#+ ORIGID RF00006_rep.3_AF045144.1/1-88_54 ORIGHEAD RF00006_rep.3
+GGCUGGCUUUAGCUCAGCGGUUACUUCGAGUACAUUGUAACCACCUCUCUGGGUGGUUCGAGACCCGCGGGUGCUUUCCAGCUCUUUU
diff -r 000000000000 -r 8ad3e79255c1 test-data/CLUSTER/1.1.cmfinder.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CLUSTER/1.1.cmfinder.fa	Fri Dec 16 07:36:24 2016 -0500
@@ -0,0 +1,120 @@
+>1.1 SEQ1#1#120#+ MERGED 1:SEQ1#1#120#+ ORIGID RF00001_rep.0_AL096764.11/46123-46004_1 ORIGHEAD RF00001_rep.0
+GUCUAUGGCCAUACCACCCUGAAUGUGCUUGAUCUCAUCUGAUCUCGUGAAGCCAAGCAGGGUGGGGCCUAGUUAGUACUUGGAUGGGAGACUUCCUGGGAAUAUAAGCUGCUGUUGGCU
+>2.1 SEQ2#1#118#+ MERGED 2:SEQ2#1#118#+ ORIGID RF00001_rep.1_U89919.1/939-1056_2 ORIGHEAD RF00001_rep.1
+CUUUACGGCCACACCACCCUGAACGCACCGGAUCUCGACUGACCUUGAAAGCUAAGCAGGAUCGGGCCUGGUUAGUAUUGGGAUGGCAGACCCCCUGGAAAUACAGGGUGCUGAAGGU
+>3.1 SEQ3#1#104#+ MERGED 3:SEQ3#1#104#+ ORIGID RF00001_rep.2_AJ508600.1/161-58_3 ORIGHEAD RF00001_rep.2
+GUCUACAGCCAUACCAUCCUGAACAUGCCAGAUCUUGUCUGACCUCUGAAGCUAAGCAGGGUCAAGCCUGGUUAGUACUUGGGAGAAGCUGGUGUGGCUAGACC
+>4.1 SEQ4#1#73#+ MERGED 4:SEQ4#1#73#+ ORIGID RF00005_rep.0_M15347.1/1040-968_4 ORIGHEAD RF00005_rep.0
+GGCUCCAUAGCUCAGGGGUUAGAGCACUGGUCUUGUAAACCAGGGGUCGCGAGUUCAAUUCUCGCUGGGGCUU
+>5.1 SEQ5#1#72#+ MERGED 5:SEQ5#1#72#+ ORIGID RF00005_rep.10_X58792.1/174-245_5 ORIGHEAD RF00005_rep.10
+GGUCCCAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUGGGACCU
+>7.1 SEQ7#1#83#+ MERGED 7:SEQ7#1#83#+ ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005_rep.12
+GUCAGGAUGGCCGAGCGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUCCCCUGGAGGCGUGGGUUCGAAUCCCACUUCUGACA
+>9.1 SEQ9#1#73#+ MERGED 9:SEQ9#1#73#+ ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005_rep.14
+GCUUCUGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCAGAAGCA
+>10.1 SEQ10#1#73#+ MERGED 10:SEQ10#1#73#+ ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005_rep.15
+GCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCG
+>11.1 SEQ11#1#82#+ MERGED 11:SEQ11#1#82#+ ORIGID RF00005_rep.16_AL133551.13/12355-12436_11 ORIGHEAD RF00005_rep.16
+GCAGCGAUGGCCGAGUGGUUAAGGCGUUGGACUUGAAAUCCAAUGGGGUCUCCCCGCGCAGGUUCGAACCCUGCUCGCUGCG
+>12.1 SEQ12#1#82#+ MERGED 12:SEQ12#1#82#+ ORIGID RF00005_rep.17_AL021918.1/54817-54736_12 ORIGHEAD RF00005_rep.17
+GUAGUCGUGGCCGAGUGGUUAAGGCGAUGGACUUGAAAUCCAUUGGGGUUUCCCCGCGCAGGUUCGAAUCCUGUCGGCUACG
+>13.1 SEQ13#1#82#+ MERGED 13:SEQ13#1#82#+ ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005_rep.18
+GUAGUCGUGGCCGAGUGGUUAAGGCGAUGGACUAGAAAUCCAUUGGGGUUUCCCCACGCAGGUUCGAAUCCUGCCGACUACG
+>14.1 SEQ14#1#73#+ MERGED 14:SEQ14#1#73#+ ORIGID RF00005_rep.19_AF134583.1/1816-1744_14 ORIGHEAD RF00005_rep.19
+UAGAUUGAAGCCAGUUGAUUAGGGUGCUUAGCUGUUAACUAAGUGUUUGUGGGUUUAAGUCCCAUUGGUCUAG
+>15.1 SEQ15#1#73#+ MERGED 15:SEQ15#1#73#+ ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005_rep.1
+GCCGAAAUAGCUCAGUUGGGAGAGCGUUAGACUGAAGAUCUAAAGGUCCCUGGUUCGAUCCCGGGUUUCGGCA
+>16.1 SEQ16#1#72#+ MERGED 16:SEQ16#1#72#+ ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005_rep.20
+GGGGAUGUAGCUCAGUGGUAGAGCGCAUGCUUCGCAUGUAUGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCA
+>17.1 SEQ17#1#71#+ MERGED 17:SEQ17#1#71#+ ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005_rep.21
+GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUCCCACGCGGGAGACCCGGGUUCAAUUCCCGGCCAAUGCA
+>18.1 SEQ18#1#72#+ MERGED 18:SEQ18#1#72#+ ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005_rep.22
+GCGUUGGUGGUAUAGUGGUGAGCAUAGCUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCAACGCA
+>19.1 SEQ19#1#82#+ MERGED 19:SEQ19#1#82#+ ORIGID RF00005_rep.23_M16479.1/42-123_19 ORIGHEAD RF00005_rep.23
+GGUGGGGUUCCCGAGCGGCCAAAGGGAGCAGACUCUAAAUCUGCCGUCAUCGACUUCGAAGGUUCGAAUCCUUCCCCCACCA
+>20.1 SEQ20#1#72#+ MERGED 20:SEQ20#1#72#+ ORIGID RF00005_rep.24_AC004941.2/32735-32806_20 ORIGHEAD RF00005_rep.24
+GGGGGUAUAGCUCAGGGGUAGAGCAUUUGACUGCAGAUCAAGAGGUCCCUGGUUCAAAUCCAGGUGCCCCCU
+>21.1 SEQ21#1#74#+ MERGED 21:SEQ21#1#74#+ ORIGID RF00005_rep.25_AC006449.19/196857-196784_21 ORIGHEAD RF00005_rep.25
+GUCUCUGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGCCCACCCAGGGACG
+>22.1 SEQ22#1#72#+ MERGED 22:SEQ22#1#72#+ ORIGID RF00005_rep.26_AF346999.1/4402-4331_22 ORIGHEAD RF00005_rep.26
+UAGGAUGGGGUGUGAUAGGUGGCACGGAGAAUUUUGGAUUCUCAGGGAUGGGUUCGAUUCUCAUAGUCCUAG
+>23.1 SEQ23#1#74#+ MERGED 23:SEQ23#1#74#+ ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005_rep.27
+GGCCGGUUAGCUCAGUUGGUUAGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCA
+>24.1 SEQ24#1#73#+ MERGED 24:SEQ24#1#73#+ ORIGID RF00005_rep.28_X04779.1/1-73_24 ORIGHEAD RF00005_rep.28
+CCUUCGAUAGCUCAGCUGGUAGAGCGGAGGACUGUAGAUCCUUAGGUCGCUGGUUCGAUUCCGGCUCGAAGGA
+>26.1 SEQ26#1#72#+ MERGED 26:SEQ26#1#72#+ ORIGID RF00005_rep.2_AL662865.4/12206-12135_26 ORIGHEAD RF00005_rep.2
+GGUUCCAUGGUGUAAUGGUUAGCACUCUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUGGAACCU
+>28.1 SEQ28#1#71#+ MERGED 28:SEQ28#1#71#+ ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005_rep.31
+GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUGCCACGCGGGAGGCCCGGGUUCGAUUCCCGGCCAAUGCA
+>30.1 SEQ30#1#72#+ MERGED 30:SEQ30#1#72#+ ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005_rep.33
+GGCUCGUUGGUCUAGGGGUAUGAUUCUCGCUUAGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCC
+>31.1 SEQ31#1#73#+ MERGED 31:SEQ31#1#73#+ ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005_rep.34
+GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCGGAAACA
+>32.1 SEQ32#1#73#+ MERGED 32:SEQ32#1#73#+ ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005_rep.35
+GUUUCCGUAGUGUAGCGGUUAUCACAUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAUCCCGGGCGGAAACA
+>33.1 SEQ33#1#72#+ MERGED 33:SEQ33#1#72#+ ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005_rep.36
+UCCUCGUUAGUAUAGUGGUGAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCGAUUCCCCGACGGGGAG
+>35.1 SEQ35#1#72#+ MERGED 35:SEQ35#1#72#+ ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005_rep.38
+UCCCUGGUGGUCUAGUGGCUAGGAUUCGGCGCUUUCACCGCCGCGCCCCGGGUUCGAUUCCCGGCCAGGAAU
+>36.1 SEQ36#1#73#+ MERGED 36:SEQ36#1#73#+ ORIGID RF00005_rep.39_AL031229.2/40502-40430_36 ORIGHEAD RF00005_rep.39
+GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUAACACGCGAAAGGUCCCUGGAUCAAAACCAGGCGGAAACA
+>37.1 SEQ37#1#82#+ MERGED 37:SEQ37#1#82#+ ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005_rep.3
+GGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGAUUUAGGCUCCAGUCUCUUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCA
+>45.1 SEQ45#1#72#+ MERGED 45:SEQ45#1#72#+ ORIGID RF00005_rep.4_Z98744.2/66305-66234_45 ORIGHEAD RF00005_rep.4
+AGCAGAGUGGCGCAGCGGAAGCGUGCUGGGCCCAUAACCCAGAGGUCGAUGGAUCGAAACCAUCCUCUGCUA
+>46.1 SEQ46#1#72#+ MERGED 46:SEQ46#1#72#+ ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005_rep.5
+UCCCUGGUGGUCUAGUGGUUAGGAUUCGGCGCUCUCACCGCCGCGGCCCGGGUUCGAUUCCCGGUCAGGGAA
+>50.1 SEQ50#1#73#+ MERGED 50:SEQ50#1#73#+ ORIGID RF00005_rep.9_AP000442.6/2022-1950_50 ORIGHEAD RF00005_rep.9
+GCCCGGAUAGCUCAGUCGGUAGAGCAUCAGACUUUUAAUCUGAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCG
+>51.1 SEQ51#1#88#+ MERGED 51:SEQ51#1#88#+ ORIGID RF00006_rep.0_AF045145.1/1-88_51 ORIGHEAD RF00006_rep.0
+GGCUGGCUUUAGCUCAGCGGUUACUUCGCGUGUCAUCAAACCACCUCUCUGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGCCCUCUU
+>52.1 SEQ52#1#101#+ MERGED 52:SEQ52#1#101#+ ORIGID RF00006_rep.1_AC005219.1/49914-50014_52 ORIGHEAD RF00006_rep.1
+GGGUCGGAGUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUGCUGGGGUUCGAGACCCGCGGGUGCUUACUGACCCUUUU
+>53.1 SEQ53#1#98#+ MERGED 53:SEQ53#1#98#+ ORIGID RF00006_rep.2_AF045143.1/1-98_53 ORIGHEAD RF00006_rep.2
+GGCUGGCUUUAGCUCAGCGGUUACUUCGACAGUUCUUUAAUUGAAACAAGCAACCUGUCUGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGUCCUUUU
+>54.1 SEQ54#1#88#+ MERGED 54:SEQ54#1#88#+ ORIGID RF00006_rep.3_AF045144.1/1-88_54 ORIGHEAD RF00006_rep.3
+GGCUGGCUUUAGCUCAGCGGUUACUUCGAGUACAUUGUAACCACCUCUCUGGGUGGUUCGAGACCCGCGGGUGCUUUCCAGCUCUUUU
+>55.1 SEQ55#1#113#+ MERGED 55:SEQ55#1#113#+ ORIGID RF00019_rep.0_V00584.1/39-151_55 ORIGHEAD RF00019_rep.0
+GGCUGGUCCGAAGGUAGUGAGUUAUCUCAAUUGAUUGUUCACAGUCAGUUACAGAUCGAACUCCUUGUUCUACUCUUUCCCCCCUUCUCACUACUGCACUUGACUAGUCUUUU
+>56.1 SEQ56#1#95#+ MERGED 56:SEQ56#1#95#+ ORIGID RF00019_rep.1_L32608.1/283-377_56 ORIGHEAD RF00019_rep.1
+GGCUGGUCCGAUGGUAGUGGGUUAUCAGAACUUAUUAACAUUAGUGUCACUAAAGUUGGUAUACAACCCCCCACUGCUAAAUUUGACUGGCUUUU
+>57.1 SEQ57#1#102#+ MERGED 57:SEQ57#1#102#+ ORIGID RF00019_rep.2_ABBA01033605.1/1707-1808_57 ORIGHEAD RF00019_rep.2
+GGCUGGUCCGAGUGCAGUGGUGUUUACAACUAAUUGAUCACAACCAGUUACAGAUUUCUUUGUUCCUUCUCCACUCCCACUGCUUCACUUGACUAGCCUUUU
+>58.1 SEQ58#1#84#+ MERGED 58:SEQ58#1#84#+ ORIGID RF00019_rep.3_AADD01087475.1/2469-2552_58 ORIGHEAD RF00019_rep.3
+AGUUGGUCCGAGUGUUGUGGGUUAUUGUUAAGUUGAUUUAACAUUGUCUCCCCCCACAACCGCGCUUGACUAGCUUGCUGUUUU
+>60.1 SEQ60#1#87#+ MERGED 60:SEQ60#1#87#+ ORIGID RF00027_rep.1_AC048341.22/3536-3622_60 ORIGHEAD RF00027_rep.1
+CCUGGCUGAGGUAGUAGUUUGUGCUGUUGGUCGGGUUGUGACAUUGCCCGCUGUGGAGAUAACUGCGCAAGCUACUGCCUUGCUAGU
+>61.1 SEQ61#1#76#+ MERGED 61:SEQ61#1#76#+ ORIGID RF00027_rep.2_AC018755.3/119936-120011_61 ORIGHEAD RF00027_rep.2
+CCGGGCUGAGGUAGGAGGUUGUAUAGUUGAGGAGGACACCCAAGGAGAUCACUAUACGGCCUCCUAGCUUUCCCCA
+>62.1 SEQ62#1#62#+ MERGED 62:SEQ62#1#62#+ ORIGID RF00031_rep.0_X71973.1/730-791_62 ORIGHEAD RF00031_rep.0
+CCGGCACUCAUGACGGCCUGCCUGCAAACCUGCUGGUGGGGCAGACCCGAAAAUCCAGCGUG
+>63.1 SEQ63#1#68#+ MERGED 63:SEQ63#1#68#+ ORIGID RF00031_rep.1_U67171.1/375-442_63 ORIGHEAD RF00031_rep.1
+GACGCUUCAUGAUAGGAAGGACUGAAAAGUCUUGUGGACACCUGGUCUUUCCCUGAUGUUCUCGUGGC
+>68.1 SEQ68#1#64#+ MERGED 68:SEQ68#1#64#+ ORIGID RF00031_rep.6_BC003127.1/865-928_68 ORIGHEAD RF00031_rep.6
+GUCACUGCAUGAUCCGCUCUGGUCAAACCCUUCCAGGCCAGCCAGAGUGGGGAUGGUCUGUGAC
+>70.1 SEQ70#1#68#+ MERGED 70:SEQ70#1#68#+ ORIGID RF00049_rep.1_X97587.1/1-68_70 ORIGHEAD RF00049_rep.1
+UUGCCAAUGAUGGUUAAGAAUUUCUUCACCGUAAUAAACCAUGUGGUCAGCAUUGCAUCUGAGGCAAA
+>72.1 SEQ72#1#126#+ MERGED 72:SEQ72#1#126#+ ORIGID RF00618_rep.0_AL135914.25/92223-92098_72 ORIGHEAD RF00618_rep.0
+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCCAAUGGGUACCUAGUGAGGGCAGUACUGCUAACUCCUGCACAACACACCGAAAUCAACUAGAGCUUUGCUUUGCCUUGGUGCAGUUUUUGGAGAA
+>73.1 SEQ73#1#126#+ MERGED 73:SEQ73#1#126#+ ORIGID RF00618_rep.1_AL161445.10/77816-77941_73 ORIGHEAD RF00618_rep.1
+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCCAAAGAGCAUGUAGUGAGGGCAGUACUGCUAACGUCUACACAACACACCCACCUCAACUAGAGCUUUGCUUUAGCUUGGUGUAAUUUUUGGAAAA
+>74.1 SEQ74#1#127#+ MERGED 74:SEQ74#1#127#+ ORIGID RF00618_rep.2_U62822.1/2-128_74 ORIGHEAD RF00618_rep.2
+ACCAUCCUUUUCUUGGGGUUGCGCUACUGUCCAAUGAGCGCAUAGUGAGGGCAGUACUGCUAACGCCUGAACAACACACCCGCAUCAACUAGAGCUUUUGCUUUAUUUUGGUGCAAUUUUUGGAAAA
+>75.1 SEQ75#1#126#+ MERGED 75:SEQ75#1#126#+ ORIGID RF00618_rep.3_AL389925.10/20736-20611_75 ORIGHEAD RF00618_rep.3
+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCUAAUGAGUGCAUAAUGAGGGCAGUAUUGCUAACGCCUAUACAAUGCACCUGCAUCAACUAGAACUUUGCUUUACCUUGGUACAAUUUUUGGAAAA
+>76.1 SEQ76#1#79#+ MERGED 76:SEQ76#1#79#+ ORIGID RF00641_rep.0_AL132709.5/95865-95787_76 ORIGHEAD RF00641_rep.0
+GGUACUUGGAGAGAGGUGGUCCGUGGCGCGUUCGCUUUAUUUAUGGCGCACAUUACACGGUCGACCUCUUUGCAGUAUC
+>77.1 SEQ77#1#77#+ MERGED 77:SEQ77#1#77#+ ORIGID RF00641_rep.10_AADD01141100.1/2839-2915_77 ORIGHEAD RF00641_rep.10
+GGUACUCGGGGAGAGGUUACCCGAGCAACUUUGCAUCUGGACGACGAAUGUUGCUCGGUGAACCCCUUUUCGGUAUC
+>80.1 SEQ80#1#79#+ MERGED 80:SEQ80#1#79#+ ORIGID RF00641_rep.13_AL132709.5/55165-55087_80 ORIGHEAD RF00641_rep.13
+GGUGCCUGAGGAGAGGUGGCCUGUGUUGCAUUCACAGAAAUCAUGACACACAAGACACGAGCGGCCUCUCUUCAGUAUC
+>82.1 SEQ82#1#81#+ MERGED 82:SEQ82#1#81#+ ORIGID RF00641_rep.2_AC208187.2/29806-29886_82 ORIGHEAD RF00641_rep.2
+GAUACUCGAAGGAGAGGUUGUCCGUGUUGUCUUCUCUUUAUUUAUGAUGAAACAUACACGGGAAACCUCUUUUUUAGUAUC
+>84.1 SEQ84#1#79#+ MERGED 84:SEQ84#1#79#+ ORIGID RF00641_rep.4_ABBA01048514.1/248685-248607_84 ORIGHEAD RF00641_rep.4
+GGUACUCGAAUGGAGGUUGUCCAUGGUGUGUUCAUUUUAUUUAUGAUGAGUAUUACAUGGCCAAUCUCCUUUCGGUACU
+>85.1 SEQ85#1#79#+ MERGED 85:SEQ85#1#79#+ ORIGID RF00641_rep.5_AL132709.5/73699-73621_85 ORIGHEAD RF00641_rep.5
+GGUGCUUAAAGAAUGGCUGUCCGUAGUAUGGUCUCUAUAUUUAUGAUGAUUAAUAUCGGACAACCAUUGUUUUAGUAUC
+>87.1 SEQ87#1#78#+ MERGED 87:SEQ87#1#78#+ ORIGID RF00641_rep.7_AL132709.5/54880-54803_87 ORIGHEAD RF00641_rep.7
+GGUACCUGAAAUAGGUUGCCUGUGAGGUGUUCACUUUCUAUAUGAUGAAUAUUAUACAGUCAACCUCUUUCCGAUAUC
+>88.1 SEQ88#1#81#+ MERGED 88:SEQ88#1#81#+ ORIGID RF00641_rep.8_AL132709.5/61554-61474_88 ORIGHEAD RF00641_rep.8
+GGUACUGGUGGAGAGGUCUUCCAUGAUGCAUUCGAUUUAUUUUUUGACCAAUCCUACAUAGUGGACUCUUUUGAAAGCAUU
diff -r 000000000000 -r 8ad3e79255c1 test-data/CLUSTER/1.1.matrix.tree
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CLUSTER/1.1.matrix.tree	Fri Dec 16 07:36:24 2016 -0500
@@ -0,0 +1,20 @@
+0.000000  0.399566  0.449067  0.416346  0.422581  0.421691  0.420328  0.433314  0.421864  0.415656  0.388584  0.396080  0.395237  0.425138  0.525331  0.428431  0.423873  0.426227  0.430509  0.421103  
+0.399566  0.000000  0.413478  0.410598  0.415992  0.448487  0.444776  0.413799  0.454424  0.422079  0.758362  0.628040  0.449935  0.432423  0.395294  0.432108  0.413869  0.394038  0.410417  0.404625  
+0.449067  0.413478  0.000000  0.447753  0.452406  0.432149  0.429802  0.446808  0.434943  0.437722  0.401281  0.400204  0.406763  0.418486  0.433646  0.417759  0.427363  0.424735  0.425622  0.422313  
+0.416346  0.410598  0.447753  0.000000  0.432407  0.413443  0.406226  0.453570  0.424393  0.406074  0.403132  0.413663  0.412748  0.409772  0.411737  0.422837  0.408136  0.419974  0.412883  0.409892  
+0.422581  0.415992  0.452406  0.432407  0.000000  0.445562  0.440880  0.457374  0.453192  0.448142  0.396150  0.415425  0.416902  0.440906  0.424893  0.433323  0.417320  0.420319  0.412897  0.417445  
+0.421691  0.448487  0.432149  0.413443  0.445562  0.000000  0.473887  0.422858  0.692833  0.442948  0.434741  0.428054  0.474703  0.466744  0.423109  0.468801  0.428776  0.430573  0.428577  0.424501  
+0.420328  0.444776  0.429802  0.406226  0.440880  0.473887  0.000000  0.423941  0.488936  0.425014  0.412393  0.417502  0.429722  0.471749  0.413970  0.438547  0.402300  0.405816  0.416556  0.412890  
+0.433314  0.413799  0.446808  0.453570  0.457374  0.422858  0.423941  0.000000  0.427433  0.436563  0.407055  0.414622  0.415155  0.429164  0.444031  0.426024  0.435089  0.420686  0.422545  0.422448  
+0.421864  0.454424  0.434943  0.424393  0.453192  0.692833  0.488936  0.427433  0.000000  0.434849  0.439028  0.434897  0.467830  0.489166  0.434846  0.473733  0.418076  0.412067  0.415370  0.421449  
+0.415656  0.422079  0.437722  0.406074  0.448142  0.442948  0.425014  0.436563  0.434849  0.000000  0.414830  0.419767  0.423499  0.443441  0.420867  0.440759  0.423357  0.422084  0.413487  0.413927  
+0.388584  0.758362  0.401281  0.403132  0.396150  0.434741  0.412393  0.407055  0.439028  0.414830  0.000000  0.826283  0.458338  0.420348  0.389570  0.431953  0.402238  0.389074  0.397992  0.391832  
+0.396080  0.628040  0.400204  0.413663  0.415425  0.428054  0.417502  0.414622  0.434897  0.419767  0.826283  0.000000  0.444033  0.419958  0.392449  0.423827  0.410142  0.395175  0.397606  0.395594  
+0.395237  0.449935  0.406763  0.412748  0.416902  0.474703  0.429722  0.415155  0.467830  0.423499  0.458338  0.444033  0.000000  0.431310  0.401528  0.447342  0.406519  0.423555  0.410966  0.407189  
+0.425138  0.432423  0.418486  0.409772  0.440906  0.466744  0.471749  0.429164  0.489166  0.443441  0.420348  0.419958  0.431310  0.000000  0.442879  0.626901  0.429861  0.419845  0.414696  0.426070  
+0.525331  0.395294  0.433646  0.411737  0.424893  0.423109  0.413970  0.444031  0.434846  0.420867  0.389570  0.392449  0.401528  0.442879  0.000000  0.452328  0.441888  0.432467  0.434868  0.431986  
+0.428431  0.432108  0.417759  0.422837  0.433323  0.468801  0.438547  0.426024  0.473733  0.440759  0.431953  0.423827  0.447342  0.626901  0.452328  0.000000  0.423858  0.419329  0.419532  0.421059  
+0.423873  0.413869  0.427363  0.408136  0.417320  0.428776  0.402300  0.435089  0.418076  0.423357  0.402238  0.410142  0.406519  0.429861  0.441888  0.423858  0.000000  0.474825  0.594380  0.571671  
+0.426227  0.394038  0.424735  0.419974  0.420319  0.430573  0.405816  0.420686  0.412067  0.422084  0.389074  0.395175  0.423555  0.419845  0.432467  0.419329  0.474825  0.000000  0.466968  0.489649  
+0.430509  0.410417  0.425622  0.412883  0.412897  0.428577  0.416556  0.422545  0.415370  0.413487  0.397992  0.397606  0.410966  0.414696  0.434868  0.419532  0.594380  0.466968  0.000000  0.548030  
+0.421103  0.404625  0.422313  0.409892  0.417445  0.424501  0.412890  0.422448  0.421449  0.413927  0.391832  0.395594  0.407189  0.426070  0.431986  0.421059  0.571671  0.489649  0.548030  0.000000  
diff -r 000000000000 -r 8ad3e79255c1 test-data/CLUSTER/1.1.tree
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CLUSTER/1.1.tree	Fri Dec 16 07:36:24 2016 -0500
@@ -0,0 +1,1 @@
+(((((54:0.133216,(53:0.115952,51:0.115952):0.0172647):0.0413516,52:0.174568):0.0233911,(37:0.150476,7:0.150476):0.047483):0.00361419,(((23:0.184455,16:0.184455):0.0038835,10:0.188338):0.00251517,15:0.190853):0.01072):0.00340405,((((46:0.099691,35:0.099691):0.0793888,((28:0.066725,17:0.066725):0.105711,18:0.172436):0.00664407):0.0153606,30:0.19444):0.00190942,(33:0.187757,((32:0,31:0):0.066541,9:0.066541):0.121216):0.00859264):0.00862737):0
diff -r 000000000000 -r 8ad3e79255c1 test-data/CLUSTER/1.2.center.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CLUSTER/1.2.center.fa	Fri Dec 16 07:36:24 2016 -0500
@@ -0,0 +1,40 @@
+>7 SEQ7#1#83#+ ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005_rep.12
+GUCAGGAUGGCCGAGCGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUCCCCUGGAGGCGUGGGUUCGAAUCCCACUUCUGACA
+>9 SEQ9#1#73#+ ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005_rep.14
+GCUUCUGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCAGAAGCA
+>10 SEQ10#1#73#+ ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005_rep.15
+GCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCG
+>15 SEQ15#1#73#+ ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005_rep.1
+GCCGAAAUAGCUCAGUUGGGAGAGCGUUAGACUGAAGAUCUAAAGGUCCCUGGUUCGAUCCCGGGUUUCGGCA
+>16 SEQ16#1#72#+ ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005_rep.20
+GGGGAUGUAGCUCAGUGGUAGAGCGCAUGCUUCGCAUGUAUGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCA
+>17 SEQ17#1#71#+ ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005_rep.21
+GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUCCCACGCGGGAGACCCGGGUUCAAUUCCCGGCCAAUGCA
+>18 SEQ18#1#72#+ ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005_rep.22
+GCGUUGGUGGUAUAGUGGUGAGCAUAGCUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCAACGCA
+>23 SEQ23#1#74#+ ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005_rep.27
+GGCCGGUUAGCUCAGUUGGUUAGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCA
+>28 SEQ28#1#71#+ ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005_rep.31
+GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUGCCACGCGGGAGGCCCGGGUUCGAUUCCCGGCCAAUGCA
+>30 SEQ30#1#72#+ ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005_rep.33
+GGCUCGUUGGUCUAGGGGUAUGAUUCUCGCUUAGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCC
+>31 SEQ31#1#73#+ ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005_rep.34
+GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCGGAAACA
+>32 SEQ32#1#73#+ ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005_rep.35
+GUUUCCGUAGUGUAGCGGUUAUCACAUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAUCCCGGGCGGAAACA
+>33 SEQ33#1#72#+ ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005_rep.36
+UCCUCGUUAGUAUAGUGGUGAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCGAUUCCCCGACGGGGAG
+>35 SEQ35#1#72#+ ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005_rep.38
+UCCCUGGUGGUCUAGUGGCUAGGAUUCGGCGCUUUCACCGCCGCGCCCCGGGUUCGAUUCCCGGCCAGGAAU
+>37 SEQ37#1#82#+ ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005_rep.3
+GGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGAUUUAGGCUCCAGUCUCUUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCA
+>46 SEQ46#1#72#+ ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005_rep.5
+UCCCUGGUGGUCUAGUGGUUAGGAUUCGGCGCUCUCACCGCCGCGGCCCGGGUUCGAUUCCCGGUCAGGGAA
+>51 SEQ51#1#88#+ ORIGID RF00006_rep.0_AF045145.1/1-88_51 ORIGHEAD RF00006_rep.0
+GGCUGGCUUUAGCUCAGCGGUUACUUCGCGUGUCAUCAAACCACCUCUCUGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGCCCUCUU
+>52 SEQ52#1#101#+ ORIGID RF00006_rep.1_AC005219.1/49914-50014_52 ORIGHEAD RF00006_rep.1
+GGGUCGGAGUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUGCUGGGGUUCGAGACCCGCGGGUGCUUACUGACCCUUUU
+>53 SEQ53#1#98#+ ORIGID RF00006_rep.2_AF045143.1/1-98_53 ORIGHEAD RF00006_rep.2
+GGCUGGCUUUAGCUCAGCGGUUACUUCGACAGUUCUUUAAUUGAAACAAGCAACCUGUCUGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGUCCUUUU
+>54 SEQ54#1#88#+ ORIGID RF00006_rep.3_AF045144.1/1-88_54 ORIGHEAD RF00006_rep.3
+GGCUGGCUUUAGCUCAGCGGUUACUUCGAGUACAUUGUAACCACCUCUCUGGGUGGUUCGAGACCCGCGGGUGCUUUCCAGCUCUUUU
diff -r 000000000000 -r 8ad3e79255c1 test-data/CLUSTER/1.2.cmfinder.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CLUSTER/1.2.cmfinder.fa	Fri Dec 16 07:36:24 2016 -0500
@@ -0,0 +1,120 @@
+>1.1 SEQ1#1#120#+ MERGED 1:SEQ1#1#120#+ ORIGID RF00001_rep.0_AL096764.11/46123-46004_1 ORIGHEAD RF00001_rep.0
+GUCUAUGGCCAUACCACCCUGAAUGUGCUUGAUCUCAUCUGAUCUCGUGAAGCCAAGCAGGGUGGGGCCUAGUUAGUACUUGGAUGGGAGACUUCCUGGGAAUAUAAGCUGCUGUUGGCU
+>2.1 SEQ2#1#118#+ MERGED 2:SEQ2#1#118#+ ORIGID RF00001_rep.1_U89919.1/939-1056_2 ORIGHEAD RF00001_rep.1
+CUUUACGGCCACACCACCCUGAACGCACCGGAUCUCGACUGACCUUGAAAGCUAAGCAGGAUCGGGCCUGGUUAGUAUUGGGAUGGCAGACCCCCUGGAAAUACAGGGUGCUGAAGGU
+>3.1 SEQ3#1#104#+ MERGED 3:SEQ3#1#104#+ ORIGID RF00001_rep.2_AJ508600.1/161-58_3 ORIGHEAD RF00001_rep.2
+GUCUACAGCCAUACCAUCCUGAACAUGCCAGAUCUUGUCUGACCUCUGAAGCUAAGCAGGGUCAAGCCUGGUUAGUACUUGGGAGAAGCUGGUGUGGCUAGACC
+>5.1 SEQ5#1#72#+ MERGED 5:SEQ5#1#72#+ ORIGID RF00005_rep.10_X58792.1/174-245_5 ORIGHEAD RF00005_rep.10
+GGUCCCAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUGGGACCU
+>6.1 SEQ6#1#66#+ MERGED 6:SEQ6#1#66#+ ORIGID RF00005_rep.11_AF346992.1/15890-15955_6 ORIGHEAD RF00005_rep.11
+GUCCUUGUAGUAUAAACUAAUACACCAGUCUUGUAAACCGGAGAUGAAAACCUUUUUCCAAGGACA
+>11.1 SEQ11#1#82#+ MERGED 11:SEQ11#1#82#+ ORIGID RF00005_rep.16_AL133551.13/12355-12436_11 ORIGHEAD RF00005_rep.16
+GCAGCGAUGGCCGAGUGGUUAAGGCGUUGGACUUGAAAUCCAAUGGGGUCUCCCCGCGCAGGUUCGAACCCUGCUCGCUGCG
+>12.1 SEQ12#1#82#+ MERGED 12:SEQ12#1#82#+ ORIGID RF00005_rep.17_AL021918.1/54817-54736_12 ORIGHEAD RF00005_rep.17
+GUAGUCGUGGCCGAGUGGUUAAGGCGAUGGACUUGAAAUCCAUUGGGGUUUCCCCGCGCAGGUUCGAAUCCUGUCGGCUACG
+>13.1 SEQ13#1#82#+ MERGED 13:SEQ13#1#82#+ ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005_rep.18
+GUAGUCGUGGCCGAGUGGUUAAGGCGAUGGACUAGAAAUCCAUUGGGGUUUCCCCACGCAGGUUCGAAUCCUGCCGACUACG
+>14.1 SEQ14#1#73#+ MERGED 14:SEQ14#1#73#+ ORIGID RF00005_rep.19_AF134583.1/1816-1744_14 ORIGHEAD RF00005_rep.19
+UAGAUUGAAGCCAGUUGAUUAGGGUGCUUAGCUGUUAACUAAGUGUUUGUGGGUUUAAGUCCCAUUGGUCUAG
+>15.1 SEQ15#1#73#+ MERGED 15:SEQ15#1#73#+ ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005_rep.1
+GCCGAAAUAGCUCAGUUGGGAGAGCGUUAGACUGAAGAUCUAAAGGUCCCUGGUUCGAUCCCGGGUUUCGGCA
+>18.1 SEQ18#1#72#+ MERGED 18:SEQ18#1#72#+ ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005_rep.22
+GCGUUGGUGGUAUAGUGGUGAGCAUAGCUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCAACGCA
+>20.1 SEQ20#1#72#+ MERGED 20:SEQ20#1#72#+ ORIGID RF00005_rep.24_AC004941.2/32735-32806_20 ORIGHEAD RF00005_rep.24
+GGGGGUAUAGCUCAGGGGUAGAGCAUUUGACUGCAGAUCAAGAGGUCCCUGGUUCAAAUCCAGGUGCCCCCU
+>22.1 SEQ22#1#72#+ MERGED 22:SEQ22#1#72#+ ORIGID RF00005_rep.26_AF346999.1/4402-4331_22 ORIGHEAD RF00005_rep.26
+UAGGAUGGGGUGUGAUAGGUGGCACGGAGAAUUUUGGAUUCUCAGGGAUGGGUUCGAUUCUCAUAGUCCUAG
+>25.1 SEQ25#1#69#+ MERGED 25:SEQ25#1#69#+ ORIGID RF00005_rep.29_AF381996.2/4265-4333_25 ORIGHEAD RF00005_rep.29
+AGAAAUAUGUCUGAUAAAAGAGUUACUUUGAUAGAGUAAAUAAUAGGAGCUUAAACCCCCUUAUUUCUA
+>26.1 SEQ26#1#72#+ MERGED 26:SEQ26#1#72#+ ORIGID RF00005_rep.2_AL662865.4/12206-12135_26 ORIGHEAD RF00005_rep.2
+GGUUCCAUGGUGUAAUGGUUAGCACUCUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUGGAACCU
+>28.1 SEQ28#1#71#+ MERGED 28:SEQ28#1#71#+ ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005_rep.31
+GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUGCCACGCGGGAGGCCCGGGUUCGAUUCCCGGCCAAUGCA
+>29.1 SEQ29#1#66#+ MERGED 29:SEQ29#1#66#+ ORIGID RF00005_rep.32_AF347015.1/5892-5827_29 ORIGHEAD RF00005_rep.32
+GGUAAAAUGGCUGAGUGAAGCAUUGGACUGUAAAUCUAAAGACAGGGGUUAGGCCUCUUUUUACCA
+>37.1 SEQ37#1#82#+ MERGED 37:SEQ37#1#82#+ ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005_rep.3
+GGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGAUUUAGGCUCCAGUCUCUUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCA
+>38.1 SEQ38#1#65#+ MERGED 38:SEQ38#1#65#+ ORIGID RF00005_rep.40_AF382013.1/10403-10467_38 ORIGHEAD RF00005_rep.40
+UGGUAUAUAGUUUAAACAAAACGAAUGAUUUCGACUCAUUAAAUUAUGAUAAUCAUAUUUACCAA
+>39.1 SEQ39#1#69#+ MERGED 39:SEQ39#1#69#+ ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005_rep.41
+GUUCUUGUAGUUGAAAUACAACGAUGGUUUUUCAUAUCAUUGGUCGUGGUUGUAGUCCGUGCGAGAAUA
+>40.1 SEQ40#1#66#+ MERGED 40:SEQ40#1#66#+ ORIGID RF00005_rep.42_AF347015.1/5827-5762_40 ORIGHEAD RF00005_rep.42
+AGCUCCGAGGUGAUUUUCAUAUUGAAUUGCAAAUUCGAAGAAGCAGCUUCAAACCUGCCGGGGCUU
+>42.1 SEQ42#1#69#+ MERGED 42:SEQ42#1#69#+ ORIGID RF00005_rep.44_AC008670.6/83597-83665_42 ORIGHEAD RF00005_rep.44
+GUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGACAACAGAGGCUCACGACCCCUUAUUUACC
+>43.1 SEQ43#1#71#+ MERGED 43:SEQ43#1#71#+ ORIGID RF00005_rep.45_AF382005.1/581-651_43 ORIGHEAD RF00005_rep.45
+GUUUAUGUAGCUUACCUCCUCAAAGCAAUACACUGAAAAUGUUUAGACGGGCUCACAUCACCCCAUAAACA
+>47.1 SEQ47#1#68#+ MERGED 47:SEQ47#1#68#+ ORIGID RF00005_rep.6_X93334.1/6942-7009_47 ORIGHEAD RF00005_rep.6
+AAGGUAUUAGAAAAACCAUUUCAUAACUUUGUCAAAGUUAAAUUAUAGGCUAAAUCCUAUAUAUCUUA
+>49.1 SEQ49#1#68#+ MERGED 49:SEQ49#1#68#+ ORIGID RF00005_rep.8_AF134583.1/1599-1666_49 ORIGHEAD RF00005_rep.8
+AGAAAUUUAGGUUAAAUACAGACCAAGAGCCUUCAAAGCCCUCAGUAAGUUGCAAUACUUAAUUUCUG
+>50.1 SEQ50#1#73#+ MERGED 50:SEQ50#1#73#+ ORIGID RF00005_rep.9_AP000442.6/2022-1950_50 ORIGHEAD RF00005_rep.9
+GCCCGGAUAGCUCAGUCGGUAGAGCAUCAGACUUUUAAUCUGAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCG
+>52.1 SEQ52#1#101#+ MERGED 52:SEQ52#1#101#+ ORIGID RF00006_rep.1_AC005219.1/49914-50014_52 ORIGHEAD RF00006_rep.1
+GGGUCGGAGUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUGCUGGGGUUCGAGACCCGCGGGUGCUUACUGACCCUUUU
+>53.1 SEQ53#1#98#+ MERGED 53:SEQ53#1#98#+ ORIGID RF00006_rep.2_AF045143.1/1-98_53 ORIGHEAD RF00006_rep.2
+GGCUGGCUUUAGCUCAGCGGUUACUUCGACAGUUCUUUAAUUGAAACAAGCAACCUGUCUGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGUCCUUUU
+>54.1 SEQ54#1#88#+ MERGED 54:SEQ54#1#88#+ ORIGID RF00006_rep.3_AF045144.1/1-88_54 ORIGHEAD RF00006_rep.3
+GGCUGGCUUUAGCUCAGCGGUUACUUCGAGUACAUUGUAACCACCUCUCUGGGUGGUUCGAGACCCGCGGGUGCUUUCCAGCUCUUUU
+>55.1 SEQ55#1#113#+ MERGED 55:SEQ55#1#113#+ ORIGID RF00019_rep.0_V00584.1/39-151_55 ORIGHEAD RF00019_rep.0
+GGCUGGUCCGAAGGUAGUGAGUUAUCUCAAUUGAUUGUUCACAGUCAGUUACAGAUCGAACUCCUUGUUCUACUCUUUCCCCCCUUCUCACUACUGCACUUGACUAGUCUUUU
+>56.1 SEQ56#1#95#+ MERGED 56:SEQ56#1#95#+ ORIGID RF00019_rep.1_L32608.1/283-377_56 ORIGHEAD RF00019_rep.1
+GGCUGGUCCGAUGGUAGUGGGUUAUCAGAACUUAUUAACAUUAGUGUCACUAAAGUUGGUAUACAACCCCCCACUGCUAAAUUUGACUGGCUUUU
+>57.1 SEQ57#1#102#+ MERGED 57:SEQ57#1#102#+ ORIGID RF00019_rep.2_ABBA01033605.1/1707-1808_57 ORIGHEAD RF00019_rep.2
+GGCUGGUCCGAGUGCAGUGGUGUUUACAACUAAUUGAUCACAACCAGUUACAGAUUUCUUUGUUCCUUCUCCACUCCCACUGCUUCACUUGACUAGCCUUUU
+>59.1 SEQ59#1#79#+ MERGED 59:SEQ59#1#79#+ ORIGID RF00027_rep.0_AF480570.1/1-79_59 ORIGHEAD RF00027_rep.0
+GUGAGGUAGUAAGUUGUAUUGUUGUGGGGUAGGGAUAUUAGGCCCCAAUUAGAAGAUAACUAUACAACUUACUACUUUC
+>60.1 SEQ60#1#87#+ MERGED 60:SEQ60#1#87#+ ORIGID RF00027_rep.1_AC048341.22/3536-3622_60 ORIGHEAD RF00027_rep.1
+CCUGGCUGAGGUAGUAGUUUGUGCUGUUGGUCGGGUUGUGACAUUGCCCGCUGUGGAGAUAACUGCGCAAGCUACUGCCUUGCUAGU
+>61.1 SEQ61#1#76#+ MERGED 61:SEQ61#1#76#+ ORIGID RF00027_rep.2_AC018755.3/119936-120011_61 ORIGHEAD RF00027_rep.2
+CCGGGCUGAGGUAGGAGGUUGUAUAGUUGAGGAGGACACCCAAGGAGAUCACUAUACGGCCUCCUAGCUUUCCCCA
+>63.1 SEQ63#1#68#+ MERGED 63:SEQ63#1#68#+ ORIGID RF00031_rep.1_U67171.1/375-442_63 ORIGHEAD RF00031_rep.1
+GACGCUUCAUGAUAGGAAGGACUGAAAAGUCUUGUGGACACCUGGUCUUUCCCUGAUGUUCUCGUGGC
+>64.1 SEQ64#1#62#+ MERGED 64:SEQ64#1#62#+ ORIGID RF00031_rep.2_S79854.1/1605-1666_64 ORIGHEAD RF00031_rep.2
+CACUGCUGAUGACGAACUAUCUCUAACUGGUCUUGACCACGAGCUAGUUCUGAAUUGCAGGG
+>66.1 SEQ66#1#71#+ MERGED 66:SEQ66#1#71#+ ORIGID RF00031_rep.4_AF195141.1/689-759_66 ORIGHEAD RF00031_rep.4
+GACUGACAUUAUGAAGGCCUGUACUGAAGACAGCAAGCUGUUAGUACAGACCAGAUGCUUUCUUGGCAGGC
+>67.1 SEQ67#1#66#+ MERGED 67:SEQ67#1#66#+ ORIGID RF00031_rep.5_AF093774.1/5851-5916_67 ORIGHEAD RF00031_rep.5
+GUGUGCGGAUGAUAACUACUGACGAAAGAGUCAUCGACCUCAGUUAGUGGUUGGAUGUAGUCACAU
+>70.1 SEQ70#1#68#+ MERGED 70:SEQ70#1#68#+ ORIGID RF00049_rep.1_X97587.1/1-68_70 ORIGHEAD RF00049_rep.1
+UUGCCAAUGAUGGUUAAGAAUUUCUUCACCGUAAUAAACCAUGUGGUCAGCAUUGCAUCUGAGGCAAA
+>72.1 SEQ72#1#126#+ MERGED 72:SEQ72#1#126#+ ORIGID RF00618_rep.0_AL135914.25/92223-92098_72 ORIGHEAD RF00618_rep.0
+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCCAAUGGGUACCUAGUGAGGGCAGUACUGCUAACUCCUGCACAACACACCGAAAUCAACUAGAGCUUUGCUUUGCCUUGGUGCAGUUUUUGGAGAA
+>73.1 SEQ73#1#126#+ MERGED 73:SEQ73#1#126#+ ORIGID RF00618_rep.1_AL161445.10/77816-77941_73 ORIGHEAD RF00618_rep.1
+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCCAAAGAGCAUGUAGUGAGGGCAGUACUGCUAACGUCUACACAACACACCCACCUCAACUAGAGCUUUGCUUUAGCUUGGUGUAAUUUUUGGAAAA
+>74.1 SEQ74#1#127#+ MERGED 74:SEQ74#1#127#+ ORIGID RF00618_rep.2_U62822.1/2-128_74 ORIGHEAD RF00618_rep.2
+ACCAUCCUUUUCUUGGGGUUGCGCUACUGUCCAAUGAGCGCAUAGUGAGGGCAGUACUGCUAACGCCUGAACAACACACCCGCAUCAACUAGAGCUUUUGCUUUAUUUUGGUGCAAUUUUUGGAAAA
+>75.1 SEQ75#1#126#+ MERGED 75:SEQ75#1#126#+ ORIGID RF00618_rep.3_AL389925.10/20736-20611_75 ORIGHEAD RF00618_rep.3
+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCUAAUGAGUGCAUAAUGAGGGCAGUAUUGCUAACGCCUAUACAAUGCACCUGCAUCAACUAGAACUUUGCUUUACCUUGGUACAAUUUUUGGAAAA
+>76.1 SEQ76#1#79#+ MERGED 76:SEQ76#1#79#+ ORIGID RF00641_rep.0_AL132709.5/95865-95787_76 ORIGHEAD RF00641_rep.0
+GGUACUUGGAGAGAGGUGGUCCGUGGCGCGUUCGCUUUAUUUAUGGCGCACAUUACACGGUCGACCUCUUUGCAGUAUC
+>77.1 SEQ77#1#77#+ MERGED 77:SEQ77#1#77#+ ORIGID RF00641_rep.10_AADD01141100.1/2839-2915_77 ORIGHEAD RF00641_rep.10
+GGUACUCGGGGAGAGGUUACCCGAGCAACUUUGCAUCUGGACGACGAAUGUUGCUCGGUGAACCCCUUUUCGGUAUC
+>78.1 SEQ78#1#80#+ MERGED 78:SEQ78#1#80#+ ORIGID RF00641_rep.11_AC208187.2/25743-25822_78 ORIGHEAD RF00641_rep.11
+GGUAUUUGAAGAUGCGGUUGACCAUGGUGUGUACGCUUUAUUUGUGACGUAGGACACAUGGUCUACUUCUUCUCAAUAUC
+>79.1 SEQ79#1#79#+ MERGED 79:SEQ79#1#79#+ ORIGID RF00641_rep.12_AL132709.5/56006-55928_79 ORIGHEAD RF00641_rep.12
+GGUACUUGAAGGGAGAUCGACCGUGUUAUAUUCGCUUUAUUGACUUCGAAUAAUACAUGGUUGAUCUUUUCUCAGUAUC
+>80.1 SEQ80#1#79#+ MERGED 80:SEQ80#1#79#+ ORIGID RF00641_rep.13_AL132709.5/55165-55087_80 ORIGHEAD RF00641_rep.13
+GGUGCCUGAGGAGAGGUGGCCUGUGUUGCAUUCACAGAAAUCAUGACACACAAGACACGAGCGGCCUCUCUUCAGUAUC
+>81.1 SEQ81#1#77#+ MERGED 81:SEQ81#1#77#+ ORIGID RF00641_rep.1_AL132709.5/86350-86274_81 ORIGHEAD RF00641_rep.1
+GGUACUGGAGGAGAGGUUAUCUGUGUUUUUUCCCUUUAUUUAUGAUGAAAAAUAUGGUGCACUUCUAUUUGAGAAUC
+>82.1 SEQ82#1#81#+ MERGED 82:SEQ82#1#81#+ ORIGID RF00641_rep.2_AC208187.2/29806-29886_82 ORIGHEAD RF00641_rep.2
+GAUACUCGAAGGAGAGGUUGUCCGUGUUGUCUUCUCUUUAUUUAUGAUGAAACAUACACGGGAAACCUCUUUUUUAGUAUC
+>84.1 SEQ84#1#79#+ MERGED 84:SEQ84#1#79#+ ORIGID RF00641_rep.4_ABBA01048514.1/248685-248607_84 ORIGHEAD RF00641_rep.4
+GGUACUCGAAUGGAGGUUGUCCAUGGUGUGUUCAUUUUAUUUAUGAUGAGUAUUACAUGGCCAAUCUCCUUUCGGUACU
+>85.1 SEQ85#1#79#+ MERGED 85:SEQ85#1#79#+ ORIGID RF00641_rep.5_AL132709.5/73699-73621_85 ORIGHEAD RF00641_rep.5
+GGUGCUUAAAGAAUGGCUGUCCGUAGUAUGGUCUCUAUAUUUAUGAUGAUUAAUAUCGGACAACCAUUGUUUUAGUAUC
+>86.1 SEQ86#1#79#+ MERGED 86:SEQ86#1#79#+ ORIGID RF00641_rep.6_AADB02234051.1/94-172_86 ORIGHEAD RF00641_rep.6
+GGUACUUAAGGGGGAGGUGGGCUUUGAAUAAUAAGUUUAUUGACGUGGAAUAUACAAGGGCAAGCUCUCUGUGAGUAUC
+>87.1 SEQ87#1#78#+ MERGED 87:SEQ87#1#78#+ ORIGID RF00641_rep.7_AL132709.5/54880-54803_87 ORIGHEAD RF00641_rep.7
+GGUACCUGAAAUAGGUUGCCUGUGAGGUGUUCACUUUCUAUAUGAUGAAUAUUAUACAGUCAACCUCUUUCCGAUAUC
+>88.1 SEQ88#1#81#+ MERGED 88:SEQ88#1#81#+ ORIGID RF00641_rep.8_AL132709.5/61554-61474_88 ORIGHEAD RF00641_rep.8
+GGUACUGGUGGAGAGGUCUUCCAUGAUGCAUUCGAUUUAUUUUUUGACCAAUCCUACAUAGUGGACUCUUUUGAAAGCAUU
+>89.1 SEQ89#1#80#+ MERGED 89:SEQ89#1#80#+ ORIGID RF00641_rep.9_AL132709.5/98273-98194_89 ORIGHEAD RF00641_rep.9
+GGUACUUGGAGAGAUAGUAGACCGUAUAGCGUACGCUUUAUCUGUGACGUAUGUAACACGGUCCACUAACCCUCAGUAUC
+>90.1 SEQ90#1#66#+ MERGED 90:SEQ90#1#66#+ ORIGID RF00693_rep.0_AADD01093451.1/1636-1571_90 ORIGHEAD RF00693_rep.0
+AAUCUUAUGGAAACAUUUCUGCACACAAUAAAGAAACUAGUGUACAGAAAUGUUUACUUGUCUAUG
+>91.1 SEQ91#1#69#+ MERGED 91:SEQ91#1#69#+ ORIGID RF00693_rep.1_AL031669.28/23303-23371_91 ORIGHEAD RF00693_rep.1
+GGUCUAGUGGAAACAUUUCUGCACAACCAGAAUACUCAAACUAGCAUGAGGAAAGGCUUCUGUAACAGU
+>92.1 SEQ92#1#69#+ MERGED 92:SEQ92#1#69#+ ORIGID RF00693_rep.2_ABBA01075050.1/41249-41181_92 ORIGHEAD RF00693_rep.2
+UAUUUCGUGGAUGAUUUCUACACAGACUAGGCCAUAGAAACCAGUGCGUAGAAAUGCUUCUGUUACAUG
diff -r 000000000000 -r 8ad3e79255c1 test-data/CLUSTER/1.2.matrix.tree
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CLUSTER/1.2.matrix.tree	Fri Dec 16 07:36:24 2016 -0500
@@ -0,0 +1,20 @@
+0.000000  0.485592  0.402363  0.407482  0.412609  0.410961  0.386728  0.446607  0.443735  0.410051  0.403386  0.393364  0.401235  0.393049  0.411519  0.403528  0.404100  0.416558  0.406340  0.399648  
+0.485592  0.000000  0.384370  0.410599  0.407923  0.407053  0.374169  0.442893  0.437057  0.406810  0.395631  0.397762  0.389239  0.392767  0.395532  0.394249  0.388597  0.412360  0.396955  0.399831  
+0.402363  0.384370  0.000000  0.406121  0.417643  0.406430  0.391946  0.407726  0.409222  0.413119  0.415314  0.374438  0.381040  0.397514  0.414524  0.408916  0.392453  0.422532  0.398895  0.386540  
+0.407482  0.410599  0.406121  0.000000  0.436926  0.493141  0.410427  0.424079  0.405272  0.414110  0.424908  0.403953  0.403042  0.408012  0.422255  0.413008  0.397386  0.430667  0.408336  0.397907  
+0.412609  0.407923  0.417643  0.436926  0.000000  0.453668  0.421291  0.434524  0.425021  0.407635  0.406622  0.388371  0.405994  0.398906  0.400531  0.423792  0.403486  0.421306  0.407819  0.403071  
+0.410961  0.407053  0.406430  0.493141  0.453668  0.000000  0.397275  0.441289  0.429696  0.403768  0.405361  0.403227  0.394256  0.398252  0.403106  0.420743  0.385639  0.417098  0.415845  0.400575  
+0.386728  0.374169  0.391946  0.410427  0.421291  0.397275  0.000000  0.385864  0.406451  0.402572  0.395132  0.379523  0.402056  0.395822  0.400937  0.393256  0.391126  0.412892  0.376576  0.375022  
+0.446607  0.442893  0.407726  0.424079  0.434524  0.441289  0.385864  0.000000  0.544420  0.412429  0.400709  0.402142  0.396695  0.410988  0.409297  0.401110  0.393163  0.422975  0.416708  0.409468  
+0.443735  0.437057  0.409222  0.405272  0.425021  0.429696  0.406451  0.544420  0.000000  0.415475  0.408533  0.392874  0.399991  0.413918  0.408149  0.409838  0.403244  0.425543  0.423586  0.405024  
+0.410051  0.406810  0.413119  0.414110  0.407635  0.403768  0.402572  0.412429  0.415475  0.000000  0.449742  0.409650  0.406410  0.414627  0.436025  0.422570  0.410786  0.426125  0.419300  0.479934  
+0.403386  0.395631  0.415314  0.424908  0.406622  0.405361  0.395132  0.400709  0.408533  0.449742  0.000000  0.400415  0.424374  0.440465  0.431290  0.428633  0.426035  0.429022  0.428411  0.437614  
+0.393364  0.397762  0.374438  0.403953  0.388371  0.403227  0.379523  0.402142  0.392874  0.409650  0.400415  0.000000  0.407757  0.429381  0.402444  0.391637  0.403821  0.448556  0.395589  0.394287  
+0.401235  0.389239  0.381040  0.403042  0.405994  0.394256  0.402056  0.396695  0.399991  0.406410  0.424374  0.407757  0.000000  0.435130  0.410495  0.408401  0.396393  0.433215  0.409976  0.407740  
+0.393049  0.392767  0.397514  0.408012  0.398906  0.398252  0.395822  0.410988  0.413918  0.414627  0.440465  0.429381  0.435130  0.000000  0.422563  0.428590  0.392764  0.428913  0.421302  0.417616  
+0.411519  0.395532  0.414524  0.422255  0.400531  0.403106  0.400937  0.409297  0.408149  0.436025  0.431290  0.402444  0.410495  0.422563  0.000000  0.410380  0.401892  0.442255  0.439551  0.394869  
+0.403528  0.394249  0.408916  0.413008  0.423792  0.420743  0.393256  0.401110  0.409838  0.422570  0.428633  0.391637  0.408401  0.428590  0.410380  0.000000  0.410693  0.428080  0.409637  0.408853  
+0.404100  0.388597  0.392453  0.397386  0.403486  0.385639  0.391126  0.393163  0.403244  0.410786  0.426035  0.403821  0.396393  0.392764  0.401892  0.410693  0.000000  0.423443  0.397289  0.413754  
+0.416558  0.412360  0.422532  0.430667  0.421306  0.417098  0.412892  0.422975  0.425543  0.426125  0.429022  0.448556  0.433215  0.428913  0.442255  0.428080  0.423443  0.000000  0.426123  0.418945  
+0.406340  0.396955  0.398895  0.408336  0.407819  0.415845  0.376576  0.416708  0.423586  0.419300  0.428411  0.395589  0.409976  0.421302  0.439551  0.409637  0.397289  0.426123  0.000000  0.392419  
+0.399648  0.399831  0.386540  0.397907  0.403071  0.400575  0.375022  0.409468  0.405024  0.479934  0.437614  0.394287  0.407740  0.417616  0.394869  0.408853  0.413754  0.418945  0.392419  0.000000  
diff -r 000000000000 -r 8ad3e79255c1 test-data/CLUSTER/1.2.tree
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CLUSTER/1.2.tree	Fri Dec 16 07:36:24 2016 -0500
@@ -0,0 +1,1 @@
+((((((((89:0.032243,78:0.032243):0.018128,79:0.050371):0.0118297,85:0.0622007):0.00232778,((88:0.0524345,84:0.0524345):0.0116038,((87:0.047932,80:0.047932):0.0118698,(82:0.054645,81:0.054645):0.00515675):0.00423656):0.000490129):0.00383806,86:0.0683665):0.00102948,(((75:0,72:0):0.0509235,(3:0.029414,1:0.029414):0.0215095):0.0122653,((57:0.0256395,55:0.0256395):0.023922,56:0.0495615):0.0136273):0.00620716):0.00172623,39:0.0711222):0.00374396,59:0.0748662):0
diff -r 000000000000 -r 8ad3e79255c1 test-data/data.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data.fasta	Fri Dec 16 07:36:24 2016 -0500
@@ -0,0 +1,184 @@
+>1 SEQ1#1#120#+ ORIGID RF00001_rep.0_AL096764.11/46123-46004_1 ORIGHEAD RF00001_rep.0
+GUCUAUGGCCAUACCACCCUGAAUGUGCUUGAUCUCAUCUGAUCUCGUGAAGCCAAGCAGGGUGGGGCCUAGUUAGUACUUGGAUGGGAGACUUCCUGGGAAUAUAAGCUGCUGUUGGCU
+>2 SEQ2#1#118#+ ORIGID RF00001_rep.1_U89919.1/939-1056_2 ORIGHEAD RF00001_rep.1
+CUUUACGGCCACACCACCCUGAACGCACCGGAUCUCGACUGACCUUGAAAGCUAAGCAGGAUCGGGCCUGGUUAGUAUUGGGAUGGCAGACCCCCUGGAAAUACAGGGUGCUGAAGGU
+>3 SEQ3#1#104#+ ORIGID RF00001_rep.2_AJ508600.1/161-58_3 ORIGHEAD RF00001_rep.2
+GUCUACAGCCAUACCAUCCUGAACAUGCCAGAUCUUGUCUGACCUCUGAAGCUAAGCAGGGUCAAGCCUGGUUAGUACUUGGGAGAAGCUGGUGUGGCUAGACC
+>4 SEQ4#1#73#+ ORIGID RF00005_rep.0_M15347.1/1040-968_4 ORIGHEAD RF00005_rep.0
+GGCUCCAUAGCUCAGGGGUUAGAGCACUGGUCUUGUAAACCAGGGGUCGCGAGUUCAAUUCUCGCUGGGGCUU
+>5 SEQ5#1#72#+ ORIGID RF00005_rep.10_X58792.1/174-245_5 ORIGHEAD RF00005_rep.10
+GGUCCCAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUGGGACCU
+>6 SEQ6#1#66#+ ORIGID RF00005_rep.11_AF346992.1/15890-15955_6 ORIGHEAD RF00005_rep.11
+GUCCUUGUAGUAUAAACUAAUACACCAGUCUUGUAAACCGGAGAUGAAAACCUUUUUCCAAGGACA
+>7 SEQ7#1#83#+ ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005_rep.12
+GUCAGGAUGGCCGAGCGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUCCCCUGGAGGCGUGGGUUCGAAUCCCACUUCUGACA
+>8 SEQ8#1#70#+ ORIGID RF00005_rep.13_AC067849.6/4771-4840_8 ORIGHEAD RF00005_rep.13
+CACUGUAAAGCUAACUUAGCAUUAACCUUUUAAGUUAAAGAUUAAGAGAACCAACACCUCUUUACAGUGA
+>9 SEQ9#1#73#+ ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005_rep.14
+GCUUCUGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCAGAAGCA
+>10 SEQ10#1#73#+ ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005_rep.15
+GCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCG
+>11 SEQ11#1#82#+ ORIGID RF00005_rep.16_AL133551.13/12355-12436_11 ORIGHEAD RF00005_rep.16
+GCAGCGAUGGCCGAGUGGUUAAGGCGUUGGACUUGAAAUCCAAUGGGGUCUCCCCGCGCAGGUUCGAACCCUGCUCGCUGCG
+>12 SEQ12#1#82#+ ORIGID RF00005_rep.17_AL021918.1/54817-54736_12 ORIGHEAD RF00005_rep.17
+GUAGUCGUGGCCGAGUGGUUAAGGCGAUGGACUUGAAAUCCAUUGGGGUUUCCCCGCGCAGGUUCGAAUCCUGUCGGCUACG
+>13 SEQ13#1#82#+ ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005_rep.18
+GUAGUCGUGGCCGAGUGGUUAAGGCGAUGGACUAGAAAUCCAUUGGGGUUUCCCCACGCAGGUUCGAAUCCUGCCGACUACG
+>14 SEQ14#1#73#+ ORIGID RF00005_rep.19_AF134583.1/1816-1744_14 ORIGHEAD RF00005_rep.19
+UAGAUUGAAGCCAGUUGAUUAGGGUGCUUAGCUGUUAACUAAGUGUUUGUGGGUUUAAGUCCCAUUGGUCUAG
+>15 SEQ15#1#73#+ ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005_rep.1
+GCCGAAAUAGCUCAGUUGGGAGAGCGUUAGACUGAAGAUCUAAAGGUCCCUGGUUCGAUCCCGGGUUUCGGCA
+>16 SEQ16#1#72#+ ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005_rep.20
+GGGGAUGUAGCUCAGUGGUAGAGCGCAUGCUUCGCAUGUAUGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCA
+>17 SEQ17#1#71#+ ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005_rep.21
+GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUCCCACGCGGGAGACCCGGGUUCAAUUCCCGGCCAAUGCA
+>18 SEQ18#1#72#+ ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005_rep.22
+GCGUUGGUGGUAUAGUGGUGAGCAUAGCUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCAACGCA
+>19 SEQ19#1#82#+ ORIGID RF00005_rep.23_M16479.1/42-123_19 ORIGHEAD RF00005_rep.23
+GGUGGGGUUCCCGAGCGGCCAAAGGGAGCAGACUCUAAAUCUGCCGUCAUCGACUUCGAAGGUUCGAAUCCUUCCCCCACCA
+>20 SEQ20#1#72#+ ORIGID RF00005_rep.24_AC004941.2/32735-32806_20 ORIGHEAD RF00005_rep.24
+GGGGGUAUAGCUCAGGGGUAGAGCAUUUGACUGCAGAUCAAGAGGUCCCUGGUUCAAAUCCAGGUGCCCCCU
+>21 SEQ21#1#74#+ ORIGID RF00005_rep.25_AC006449.19/196857-196784_21 ORIGHEAD RF00005_rep.25
+GUCUCUGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGCCCACCCAGGGACG
+>22 SEQ22#1#72#+ ORIGID RF00005_rep.26_AF346999.1/4402-4331_22 ORIGHEAD RF00005_rep.26
+UAGGAUGGGGUGUGAUAGGUGGCACGGAGAAUUUUGGAUUCUCAGGGAUGGGUUCGAUUCUCAUAGUCCUAG
+>23 SEQ23#1#74#+ ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005_rep.27
+GGCCGGUUAGCUCAGUUGGUUAGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCA
+>24 SEQ24#1#73#+ ORIGID RF00005_rep.28_X04779.1/1-73_24 ORIGHEAD RF00005_rep.28
+CCUUCGAUAGCUCAGCUGGUAGAGCGGAGGACUGUAGAUCCUUAGGUCGCUGGUUCGAUUCCGGCUCGAAGGA
+>25 SEQ25#1#69#+ ORIGID RF00005_rep.29_AF381996.2/4265-4333_25 ORIGHEAD RF00005_rep.29
+AGAAAUAUGUCUGAUAAAAGAGUUACUUUGAUAGAGUAAAUAAUAGGAGCUUAAACCCCCUUAUUUCUA
+>26 SEQ26#1#72#+ ORIGID RF00005_rep.2_AL662865.4/12206-12135_26 ORIGHEAD RF00005_rep.2
+GGUUCCAUGGUGUAAUGGUUAGCACUCUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUGGAACCU
+>27 SEQ27#1#69#+ ORIGID RF00005_rep.30_AL132988.4/95773-95841_27 ORIGHEAD RF00005_rep.30
+AAGGGCUUAGCUUAAUUAAAGUGGCUGAUUUGCGUUCAGUUGAUGCAGAGUGGGGUUUUGCAGUCCUUA
+>28 SEQ28#1#71#+ ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005_rep.31
+GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUGCCACGCGGGAGGCCCGGGUUCGAUUCCCGGCCAAUGCA
+>29 SEQ29#1#66#+ ORIGID RF00005_rep.32_AF347015.1/5892-5827_29 ORIGHEAD RF00005_rep.32
+GGUAAAAUGGCUGAGUGAAGCAUUGGACUGUAAAUCUAAAGACAGGGGUUAGGCCUCUUUUUACCA
+>30 SEQ30#1#72#+ ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005_rep.33
+GGCUCGUUGGUCUAGGGGUAUGAUUCUCGCUUAGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCC
+>31 SEQ31#1#73#+ ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005_rep.34
+GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCGGAAACA
+>32 SEQ32#1#73#+ ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005_rep.35
+GUUUCCGUAGUGUAGCGGUUAUCACAUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAUCCCGGGCGGAAACA
+>33 SEQ33#1#72#+ ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005_rep.36
+UCCUCGUUAGUAUAGUGGUGAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCGAUUCCCCGACGGGGAG
+>34 SEQ34#1#68#+ ORIGID RF00005_rep.37_AF347001.1/16015-15948_34 ORIGHEAD RF00005_rep.37
+CAGAGAAUAGUUUAAAUUAGAAUCUUAGCUUUGGGUGCUAAUGGUGGAGUUAAAGACUUUUUCUCUGA
+>35 SEQ35#1#72#+ ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005_rep.38
+UCCCUGGUGGUCUAGUGGCUAGGAUUCGGCGCUUUCACCGCCGCGCCCCGGGUUCGAUUCCCGGCCAGGAAU
+>36 SEQ36#1#73#+ ORIGID RF00005_rep.39_AL031229.2/40502-40430_36 ORIGHEAD RF00005_rep.39
+GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUAACACGCGAAAGGUCCCUGGAUCAAAACCAGGCGGAAACA
+>37 SEQ37#1#82#+ ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005_rep.3
+GGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGAUUUAGGCUCCAGUCUCUUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCA
+>38 SEQ38#1#65#+ ORIGID RF00005_rep.40_AF382013.1/10403-10467_38 ORIGHEAD RF00005_rep.40
+UGGUAUAUAGUUUAAACAAAACGAAUGAUUUCGACUCAUUAAAUUAUGAUAAUCAUAUUUACCAA
+>39 SEQ39#1#69#+ ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005_rep.41
+GUUCUUGUAGUUGAAAUACAACGAUGGUUUUUCAUAUCAUUGGUCGUGGUUGUAGUCCGUGCGAGAAUA
+>40 SEQ40#1#66#+ ORIGID RF00005_rep.42_AF347015.1/5827-5762_40 ORIGHEAD RF00005_rep.42
+AGCUCCGAGGUGAUUUUCAUAUUGAAUUGCAAAUUCGAAGAAGCAGCUUCAAACCUGCCGGGGCUU
+>41 SEQ41#1#68#+ ORIGID RF00005_rep.43_L23320.1/77-10_41 ORIGHEAD RF00005_rep.43
+ACUCUUUUAGUAUAAAUAGUACCGUUAACUUCCAAUUAACUAGUUUUGACAACAUUCAAAAAAGAGUA
+>42 SEQ42#1#69#+ ORIGID RF00005_rep.44_AC008670.6/83597-83665_42 ORIGHEAD RF00005_rep.44
+GUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGACAACAGAGGCUCACGACCCCUUAUUUACC
+>43 SEQ43#1#71#+ ORIGID RF00005_rep.45_AF382005.1/581-651_43 ORIGHEAD RF00005_rep.45
+GUUUAUGUAGCUUACCUCCUCAAAGCAAUACACUGAAAAUGUUUAGACGGGCUCACAUCACCCCAUAAACA
+>44 SEQ44#1#69#+ ORIGID RF00005_rep.46_AF347015.1/1604-1672_44 ORIGHEAD RF00005_rep.46
+CAGAGUGUAGCUUAACACAAAGCACCCAACUUACACUUAGGAGAUUUCAACUUAACUUGACCGCUCUGA
+>45 SEQ45#1#72#+ ORIGID RF00005_rep.4_Z98744.2/66305-66234_45 ORIGHEAD RF00005_rep.4
+AGCAGAGUGGCGCAGCGGAAGCGUGCUGGGCCCAUAACCCAGAGGUCGAUGGAUCGAAACCAUCCUCUGCUA
+>46 SEQ46#1#72#+ ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005_rep.5
+UCCCUGGUGGUCUAGUGGUUAGGAUUCGGCGCUCUCACCGCCGCGGCCCGGGUUCGAUUCCCGGUCAGGGAA
+>47 SEQ47#1#68#+ ORIGID RF00005_rep.6_X93334.1/6942-7009_47 ORIGHEAD RF00005_rep.6
+AAGGUAUUAGAAAAACCAUUUCAUAACUUUGUCAAAGUUAAAUUAUAGGCUAAAUCCUAUAUAUCUUA
+>48 SEQ48#1#71#+ ORIGID RF00005_rep.7_AF347005.1/12268-12338_48 ORIGHEAD RF00005_rep.7
+ACUUUUAAAGGAUAACAGCUAUCCAUUGGUCUUAGGCCCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUA
+>49 SEQ49#1#68#+ ORIGID RF00005_rep.8_AF134583.1/1599-1666_49 ORIGHEAD RF00005_rep.8
+AGAAAUUUAGGUUAAAUACAGACCAAGAGCCUUCAAAGCCCUCAGUAAGUUGCAAUACUUAAUUUCUG
+>50 SEQ50#1#73#+ ORIGID RF00005_rep.9_AP000442.6/2022-1950_50 ORIGHEAD RF00005_rep.9
+GCCCGGAUAGCUCAGUCGGUAGAGCAUCAGACUUUUAAUCUGAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCG
+>51 SEQ51#1#88#+ ORIGID RF00006_rep.0_AF045145.1/1-88_51 ORIGHEAD RF00006_rep.0
+GGCUGGCUUUAGCUCAGCGGUUACUUCGCGUGUCAUCAAACCACCUCUCUGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGCCCUCUU
+>52 SEQ52#1#101#+ ORIGID RF00006_rep.1_AC005219.1/49914-50014_52 ORIGHEAD RF00006_rep.1
+GGGUCGGAGUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUGCUGGGGUUCGAGACCCGCGGGUGCUUACUGACCCUUUU
+>53 SEQ53#1#98#+ ORIGID RF00006_rep.2_AF045143.1/1-98_53 ORIGHEAD RF00006_rep.2
+GGCUGGCUUUAGCUCAGCGGUUACUUCGACAGUUCUUUAAUUGAAACAAGCAACCUGUCUGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGUCCUUUU
+>54 SEQ54#1#88#+ ORIGID RF00006_rep.3_AF045144.1/1-88_54 ORIGHEAD RF00006_rep.3
+GGCUGGCUUUAGCUCAGCGGUUACUUCGAGUACAUUGUAACCACCUCUCUGGGUGGUUCGAGACCCGCGGGUGCUUUCCAGCUCUUUU
+>55 SEQ55#1#113#+ ORIGID RF00019_rep.0_V00584.1/39-151_55 ORIGHEAD RF00019_rep.0
+GGCUGGUCCGAAGGUAGUGAGUUAUCUCAAUUGAUUGUUCACAGUCAGUUACAGAUCGAACUCCUUGUUCUACUCUUUCCCCCCUUCUCACUACUGCACUUGACUAGUCUUUU
+>56 SEQ56#1#95#+ ORIGID RF00019_rep.1_L32608.1/283-377_56 ORIGHEAD RF00019_rep.1
+GGCUGGUCCGAUGGUAGUGGGUUAUCAGAACUUAUUAACAUUAGUGUCACUAAAGUUGGUAUACAACCCCCCACUGCUAAAUUUGACUGGCUUUU
+>57 SEQ57#1#102#+ ORIGID RF00019_rep.2_ABBA01033605.1/1707-1808_57 ORIGHEAD RF00019_rep.2
+GGCUGGUCCGAGUGCAGUGGUGUUUACAACUAAUUGAUCACAACCAGUUACAGAUUUCUUUGUUCCUUCUCCACUCCCACUGCUUCACUUGACUAGCCUUUU
+>58 SEQ58#1#84#+ ORIGID RF00019_rep.3_AADD01087475.1/2469-2552_58 ORIGHEAD RF00019_rep.3
+AGUUGGUCCGAGUGUUGUGGGUUAUUGUUAAGUUGAUUUAACAUUGUCUCCCCCCACAACCGCGCUUGACUAGCUUGCUGUUUU
+>59 SEQ59#1#79#+ ORIGID RF00027_rep.0_AF480570.1/1-79_59 ORIGHEAD RF00027_rep.0
+GUGAGGUAGUAAGUUGUAUUGUUGUGGGGUAGGGAUAUUAGGCCCCAAUUAGAAGAUAACUAUACAACUUACUACUUUC
+>60 SEQ60#1#87#+ ORIGID RF00027_rep.1_AC048341.22/3536-3622_60 ORIGHEAD RF00027_rep.1
+CCUGGCUGAGGUAGUAGUUUGUGCUGUUGGUCGGGUUGUGACAUUGCCCGCUGUGGAGAUAACUGCGCAAGCUACUGCCUUGCUAGU
+>61 SEQ61#1#76#+ ORIGID RF00027_rep.2_AC018755.3/119936-120011_61 ORIGHEAD RF00027_rep.2
+CCGGGCUGAGGUAGGAGGUUGUAUAGUUGAGGAGGACACCCAAGGAGAUCACUAUACGGCCUCCUAGCUUUCCCCA
+>62 SEQ62#1#62#+ ORIGID RF00031_rep.0_X71973.1/730-791_62 ORIGHEAD RF00031_rep.0
+CCGGCACUCAUGACGGCCUGCCUGCAAACCUGCUGGUGGGGCAGACCCGAAAAUCCAGCGUG
+>63 SEQ63#1#68#+ ORIGID RF00031_rep.1_U67171.1/375-442_63 ORIGHEAD RF00031_rep.1
+GACGCUUCAUGAUAGGAAGGACUGAAAAGUCUUGUGGACACCUGGUCUUUCCCUGAUGUUCUCGUGGC
+>64 SEQ64#1#62#+ ORIGID RF00031_rep.2_S79854.1/1605-1666_64 ORIGHEAD RF00031_rep.2
+CACUGCUGAUGACGAACUAUCUCUAACUGGUCUUGACCACGAGCUAGUUCUGAAUUGCAGGG
+>65 SEQ65#1#57#+ ORIGID RF00031_rep.3_X53463.1/847-903_65 ORIGHEAD RF00031_rep.3
+UUCACAGAAUGAUGGCACCUUCCUAAACCCUCAUGGGUGGUGUCUGAGAGGCGUGAA
+>66 SEQ66#1#71#+ ORIGID RF00031_rep.4_AF195141.1/689-759_66 ORIGHEAD RF00031_rep.4
+GACUGACAUUAUGAAGGCCUGUACUGAAGACAGCAAGCUGUUAGUACAGACCAGAUGCUUUCUUGGCAGGC
+>67 SEQ67#1#66#+ ORIGID RF00031_rep.5_AF093774.1/5851-5916_67 ORIGHEAD RF00031_rep.5
+GUGUGCGGAUGAUAACUACUGACGAAAGAGUCAUCGACCUCAGUUAGUGGUUGGAUGUAGUCACAU
+>68 SEQ68#1#64#+ ORIGID RF00031_rep.6_BC003127.1/865-928_68 ORIGHEAD RF00031_rep.6
+GUCACUGCAUGAUCCGCUCUGGUCAAACCCUUCCAGGCCAGCCAGAGUGGGGAUGGUCUGUGAC
+>69 SEQ69#1#82#+ ORIGID RF00049_rep.0_X52138.1/3930-4011_69 ORIGHEAD RF00049_rep.0
+CAGCAGUCGAUCGUCAAAAUUUCUUCGGCCUCGAAAUUCACUCGUCGAAGAGUCAAAACCGAGCUUUUUAACACUGAGUCAG
+>70 SEQ70#1#68#+ ORIGID RF00049_rep.1_X97587.1/1-68_70 ORIGHEAD RF00049_rep.1
+UUGCCAAUGAUGGUUAAGAAUUUCUUCACCGUAAUAAACCAUGUGGUCAGCAUUGCAUCUGAGGCAAA
+>71 SEQ71#1#76#+ ORIGID RF00049_rep.2_X61923.1/2094-2169_71 ORIGHEAD RF00049_rep.2
+UAGCAGUCGAUGUCAAAAUUUCUUGGCUCGAAAUUACUGUGAAGAGUAAAAUCGAGCUUUUUAAGAGUGAGUCAGC
+>72 SEQ72#1#126#+ ORIGID RF00618_rep.0_AL135914.25/92223-92098_72 ORIGHEAD RF00618_rep.0
+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCCAAUGGGUACCUAGUGAGGGCAGUACUGCUAACUCCUGCACAACACACCGAAAUCAACUAGAGCUUUGCUUUGCCUUGGUGCAGUUUUUGGAGAA
+>73 SEQ73#1#126#+ ORIGID RF00618_rep.1_AL161445.10/77816-77941_73 ORIGHEAD RF00618_rep.1
+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCCAAAGAGCAUGUAGUGAGGGCAGUACUGCUAACGUCUACACAACACACCCACCUCAACUAGAGCUUUGCUUUAGCUUGGUGUAAUUUUUGGAAAA
+>74 SEQ74#1#127#+ ORIGID RF00618_rep.2_U62822.1/2-128_74 ORIGHEAD RF00618_rep.2
+ACCAUCCUUUUCUUGGGGUUGCGCUACUGUCCAAUGAGCGCAUAGUGAGGGCAGUACUGCUAACGCCUGAACAACACACCCGCAUCAACUAGAGCUUUUGCUUUAUUUUGGUGCAAUUUUUGGAAAA
+>75 SEQ75#1#126#+ ORIGID RF00618_rep.3_AL389925.10/20736-20611_75 ORIGHEAD RF00618_rep.3
+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCUAAUGAGUGCAUAAUGAGGGCAGUAUUGCUAACGCCUAUACAAUGCACCUGCAUCAACUAGAACUUUGCUUUACCUUGGUACAAUUUUUGGAAAA
+>76 SEQ76#1#79#+ ORIGID RF00641_rep.0_AL132709.5/95865-95787_76 ORIGHEAD RF00641_rep.0
+GGUACUUGGAGAGAGGUGGUCCGUGGCGCGUUCGCUUUAUUUAUGGCGCACAUUACACGGUCGACCUCUUUGCAGUAUC
+>77 SEQ77#1#77#+ ORIGID RF00641_rep.10_AADD01141100.1/2839-2915_77 ORIGHEAD RF00641_rep.10
+GGUACUCGGGGAGAGGUUACCCGAGCAACUUUGCAUCUGGACGACGAAUGUUGCUCGGUGAACCCCUUUUCGGUAUC
+>78 SEQ78#1#80#+ ORIGID RF00641_rep.11_AC208187.2/25743-25822_78 ORIGHEAD RF00641_rep.11
+GGUAUUUGAAGAUGCGGUUGACCAUGGUGUGUACGCUUUAUUUGUGACGUAGGACACAUGGUCUACUUCUUCUCAAUAUC
+>79 SEQ79#1#79#+ ORIGID RF00641_rep.12_AL132709.5/56006-55928_79 ORIGHEAD RF00641_rep.12
+GGUACUUGAAGGGAGAUCGACCGUGUUAUAUUCGCUUUAUUGACUUCGAAUAAUACAUGGUUGAUCUUUUCUCAGUAUC
+>80 SEQ80#1#79#+ ORIGID RF00641_rep.13_AL132709.5/55165-55087_80 ORIGHEAD RF00641_rep.13
+GGUGCCUGAGGAGAGGUGGCCUGUGUUGCAUUCACAGAAAUCAUGACACACAAGACACGAGCGGCCUCUCUUCAGUAUC
+>81 SEQ81#1#77#+ ORIGID RF00641_rep.1_AL132709.5/86350-86274_81 ORIGHEAD RF00641_rep.1
+GGUACUGGAGGAGAGGUUAUCUGUGUUUUUUCCCUUUAUUUAUGAUGAAAAAUAUGGUGCACUUCUAUUUGAGAAUC
+>82 SEQ82#1#81#+ ORIGID RF00641_rep.2_AC208187.2/29806-29886_82 ORIGHEAD RF00641_rep.2
+GAUACUCGAAGGAGAGGUUGUCCGUGUUGUCUUCUCUUUAUUUAUGAUGAAACAUACACGGGAAACCUCUUUUUUAGUAUC
+>83 SEQ83#1#79#+ ORIGID RF00641_rep.3_AADD01141098.1/2614-2692_83 ORIGHEAD RF00641_rep.3
+GCUACUUGAAGAGAGGUAAUCCUUCAUGCAUUUGCUUUACUUGCAAUGAUUAUACAAGGGCAGACUCUCUCUGGGGAGC
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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