bio 1.3.1 → 1.4.0

data/test/data/fastq/misc_dna_original_sanger.fastq

@@ -0,0 +1,16 @@
+@FAKE0007 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
+@FAKE0008 Original version has mixed case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
+gTcatAGcgTcatAGcgTcatAGcgTcatAGcgTcatAGcg
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
+@FAKE0009 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
+tcagtcagtcagtcagtcagtcagtcagtcagtcagtcagt
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
+@FAKE0010 Original version has mixed case ambiguous DNA and PHRED scores of 40, 30, 20, 10 (cycled)
+gatcrywsmkhbvdnGATCRYWSMKHBVDN
++
+I?5+I?5+I?5+I?5+I?5+I?5+I?5+I?

data/test/data/fastq/misc_rna_as_illumina.fastq

@@ -0,0 +1,16 @@
+@FAKE0011 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
+ACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUA
++
+@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
+@FAKE0012 Original version has mixed case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
+gUcauAGcgUcauAGcgUcauAGcgUcauAGcgUcauAGcg
++
+@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
+@FAKE0013 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
+ucagucagucagucagucagucagucagucagucagucagu
++
+@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
+@FAKE0014 Original version has mixed case ambiguous RNA with PHRED scores from 35 to 40 inclusive (cycled)
+gaucrywsmkhbvdnGAUCRYWSMKHBVDN
++
+cdefghcdefghcdefghcdefghcdefgh

data/test/data/fastq/misc_rna_as_sanger.fastq

@@ -0,0 +1,16 @@
+@FAKE0011 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
+ACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUA
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
+@FAKE0012 Original version has mixed case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
+gUcauAGcgUcauAGcgUcauAGcgUcauAGcgUcauAGcg
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
+@FAKE0013 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
+ucagucagucagucagucagucagucagucagucagucagu
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
+@FAKE0014 Original version has mixed case ambiguous RNA with PHRED scores from 35 to 40 inclusive (cycled)
+gaucrywsmkhbvdnGAUCRYWSMKHBVDN
++
+DEFGHIDEFGHIDEFGHIDEFGHIDEFGHI

data/test/data/fastq/misc_rna_as_solexa.fastq

@@ -0,0 +1,16 @@
+@FAKE0011 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
+ACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUA
++
+;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
+@FAKE0012 Original version has mixed case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
+gUcauAGcgUcauAGcgUcauAGcgUcauAGcgUcauAGcg
++
+;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
+@FAKE0013 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
+ucagucagucagucagucagucagucagucagucagucagu
++
+;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
+@FAKE0014 Original version has mixed case ambiguous RNA with PHRED scores from 35 to 40 inclusive (cycled)
+gaucrywsmkhbvdnGAUCRYWSMKHBVDN
++
+cdefghcdefghcdefghcdefghcdefgh

data/test/data/fastq/misc_rna_original_sanger.fastq

@@ -0,0 +1,16 @@
+@FAKE0011 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
+ACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUA
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
+@FAKE0012 Original version has mixed case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
+gUcauAGcgUcauAGcgUcauAGcgUcauAGcgUcauAGcg
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
+@FAKE0013 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
+ucagucagucagucagucagucagucagucagucagucagu
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
+@FAKE0014 Original version has mixed case ambiguous RNA with PHRED scores from 35 to 40 inclusive (cycled)
+gaucrywsmkhbvdnGAUCRYWSMKHBVDN
++
+DEFGHIDEFGHIDEFGHIDEFGHIDEFGHI

data/test/data/fastq/sanger_full_range_as_illumina.fastq

@@ -0,0 +1,8 @@
+@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order)
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
++
+@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order)
+CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@

data/test/data/fastq/sanger_full_range_as_sanger.fastq

@@ -0,0 +1,8 @@
+@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order)
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
+@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order)
+CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
++
+~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!

data/test/data/fastq/sanger_full_range_as_solexa.fastq

@@ -0,0 +1,8 @@
+@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order)
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
++
+;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order)
+CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJHGFECB@>;;

data/test/data/fastq/sanger_full_range_original_sanger.fastq

@@ -0,0 +1,8 @@
+@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order)
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
+@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order)
+CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
++
+~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!

data/test/data/fastq/solexa_full_range_as_illumina.fastq

@@ -0,0 +1,8 @@
+@FAKE0003 Original version has Solexa scores from -5 to 62 inclusive (in that order)
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
++
+AABBCCDDEEFGHIJJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
+@FAKE0004 Original version has Solexa scores from 62 to -5 inclusive (in that order)
+TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
++
+~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJJIHGFEEDDCCBBAA

data/test/data/fastq/solexa_full_range_as_sanger.fastq

@@ -0,0 +1,8 @@
+@FAKE0003 Original version has Solexa scores from -5 to 62 inclusive (in that order)
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
++
+""##$$%%&&'()*++,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_
+@FAKE0004 Original version has Solexa scores from 62 to -5 inclusive (in that order)
+TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
++
+_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,++*)('&&%%$$##""

data/test/data/fastq/solexa_full_range_as_solexa.fastq

@@ -0,0 +1,8 @@
+@FAKE0003 Original version has Solexa scores from -5 to 62 inclusive (in that order)
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
++
+;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
+@FAKE0004 Original version has Solexa scores from 62 to -5 inclusive (in that order)
+TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
++
+~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;

data/test/data/fastq/solexa_full_range_original_solexa.fastq

@@ -0,0 +1,8 @@
+@FAKE0003 Original version has Solexa scores from -5 to 62 inclusive (in that order)
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
++
+;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
+@FAKE0004 Original version has Solexa scores from 62 to -5 inclusive (in that order)
+TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
++
+~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;

data/test/data/fastq/wrapping_as_illumina.fastq

@@ -0,0 +1,12 @@
+@SRR014849.50939 EIXKN4201BA2EC length=135
+GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG
++
+Zb^Ld`N\[d`NaZ[aZc]UOKHDA[\YT[_W[aZ\aZ[Zd`SF_WeaUI[Y\[[\\\[\Z\aY`X[[aZ\aZ\d`OY[aY[[\[[e`WPJC^UZ[`X\[R]T_V_W[`[Ga\I`\H[[Q^TVa\Ia\Ic^LY\S
+@SRR014849.110027 EIXKN4201APUB0 length=131
+CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG
++
+\aYY_[FY\T`X^Vd`OY\[[^U_V[R^T[_ZDc^La\HYYO\S[c^Ld`Nc_QAZaZaYaY`XZZ\[aZZ[aZ[aZ[aZY`Z[`ZWeaVJ\[aZaY`X[PY\eaUG[\[[d`OXTUZ[Q\\`W\\\Y_W\
+@SRR014849.203935 EIXKN4201B4HU6 length=144
+AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT
++
+`Z_ZDVT^YB[[Xd`PZ\d`RDaZaZ`ZaZ_ZDXd`Pd`Pd`RD[aZ`ZWd`Oc_RCd`P\aZ`ZaZaZY\YaZYaY`XYd`O`X[e`WPJEAc^LaZS[YYN[Z\Y`XWLT^U\b]JW[[RZ\SYc`RD[Z\WLXM`\HYa\I

data/test/data/fastq/wrapping_as_sanger.fastq

@@ -0,0 +1,12 @@
+@SRR014849.50939 EIXKN4201BA2EC length=135
+GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG
++
+;C?-EA/=<EA/B;<B;D>60,)%"<=:5<@8<B;=B;<;EA4'@8FB6*<:=<<===<=;=B:A9<<B;=B;=EA0:<B:<<=<<FA81+$?6;<A9=<3>5@7@8<A<(B=*A=)<<2?57B=*B=*D?-:=4
+@SRR014849.110027 EIXKN4201APUB0 length=131
+CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG
++
+=B::@<':=5A9?7EA0:=<<?6@7<3?5<@;%D?-B=)::0=4<D?-EA/D@2";B;B:B:A9;;=<B;;<B;<B;<B;:A;<A;8FB7+=<B;B:A9<1:=FB6(<=<<EA0956;<2==A8===:@8=
+@SRR014849.203935 EIXKN4201B4HU6 length=144
+AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT
++
+A;@;%75?:#<<9EA1;=EA3%B;B;A;B;@;%9EA1EA1EA3%<B;A;8EA0D@3$EA1=B;A;B;B;:=:B;:B:A9:EA0A9<FA81+&"D?-B;4<::/<;=:A98-5?6=C>+8<<3;=4:DA3%<;=8-9.A=):B=*

data/test/data/fastq/wrapping_as_solexa.fastq

@@ -0,0 +1,12 @@
+@SRR014849.50939 EIXKN4201BA2EC length=135
+GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG
++
+Zb^Ld`N\[d`NaZ[aZc]UOKGB;[\YT[_W[aZ\aZ[Zd`SE_WeaUH[Y\[[\\\[\Z\aY`X[[aZ\aZ\d`OY[aY[[\[[e`WPJ@^UZ[`X\[R]T_V_W[`[Fa\H`\G[[Q^TVa\Ha\Hc^LY\S
+@SRR014849.110027 EIXKN4201APUB0 length=131
+CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG
++
+\aYY_[EY\T`X^Vd`OY\[[^U_V[R^T[_ZBc^La\GYYO\S[c^Ld`Nc_Q;ZaZaYaY`XZZ\[aZZ[aZ[aZ[aZY`Z[`ZWeaVJ\[aZaY`X[PY\eaUF[\[[d`OXTUZ[Q\\`W\\\Y_W\
+@SRR014849.203935 EIXKN4201B4HU6 length=144
+AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT
++
+`Z_ZBVT^Y>[[Xd`PZ\d`RBaZaZ`ZaZ_ZBXd`Pd`Pd`RB[aZ`ZWd`Oc_R@d`P\aZ`ZaZaZY\YaZYaY`XYd`O`X[e`WPJC;c^LaZS[YYN[Z\Y`XWLT^U\b]JW[[RZ\SYc`RB[Z\WLXM`\GYa\H

data/test/data/fastq/wrapping_original_sanger.fastq

@@ -0,0 +1,24 @@
+@SRR014849.50939 EIXKN4201BA2EC length=135
+GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG
++
+;C?-EA/=<EA/B;<B;D>60,)%"<=:5<
+@8<B;=B;<;EA4'@8FB6*<:=<<===<=
+;=B:A9<<B;=B;=EA0:<B:<<=<<FA81
++$?6;<A9=<3>5@7@8<A<(B=*A=)<<2
+?57B=*B=*D?-:=4
+@SRR014849.110027 EIXKN4201APUB0 length=131
+CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG
++
+=B::@<':=5A9?7EA0:=<<?6@7<3?5<
+@;%D?-B=)::0=4<D?-EA/D@2";B;B:
+B:A9;;=<B;;<B;<B;<B;:A;<A;8FB7
++=<B;B:A9<1:=FB6(<=<<EA0956;<2
+==A8===:@8=
+@SRR014849.203935 EIXKN4201B4HU6 length=144
+AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT
++
+A;@;%75?:#<<9EA1;=EA3%B;B;A;B;
+@;%9EA1EA1EA3%<B;A;8EA0D@3$EA1
+=B;A;B;B;:=:B;:B:A9:EA0A9<FA81
++&"D?-B;4<::/<;=:A98-5?6=C>+8<
+<3;=4:DA3%<;=8-9.A=):B=*

data/test/data/meme/mast.out

@@ -0,0 +1,13 @@
+# All non-overlapping hits in all sequences.
+# sequence_name motif hit_start hit_end hit_p-value
+gi|33357914|pdb|1P85|M 6 54 74 3.70e-05
+gi|14488684|pdb|1IHO|A 2 195 215 3.12e-05
+gi|2624640|pdb|1HXQ|B 1 173 220 4.27e-05
+gi|9954928|pdb|1EYZ|A 6 7 27 2.72e-05
+gi|9954928|pdb|1EYZ|A 10 311 325 9.75e-05
+gi|28948818|pdb|1NEK|A 2 29 49 8.96e-06
+gi|85544130|pdb|2AVU|E 8 112 140 4.25e-05
+gi|83754486|pdb|2C27|A 6 42 62 2.72e-05
+gi|18655936|pdb|1KP9|A 8 92 120 3.96e-05
+gi|88192540|pdb|2C4N|A 8 178 206 5.42e-05
+gi|157831485|pdb|1IOV|A 3 130 150 6.63e-07

data/test/data/meme/meme.out

@@ -0,0 +1,3 @@
+********************************************************************************
+MEME - Motif discovery tool
+********************************************************************************

data/test/data/phyloxml/apaf.xml

@@ -0,0 +1,666 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.00/phyloxml.xsd" xmlns="http://www.phyloxml.org">
+<phylogeny rooted="true">
+   <clade>
+      <clade>
+         <branch_length>0.18105</branch_length>
+         <confidence type="unknown">89.0</confidence>
+         <clade>
+            <branch_length>0.07466</branch_length>
+            <confidence type="unknown">32.0</confidence>
+            <clade>
+               <branch_length>0.26168</branch_length>
+               <confidence type="unknown">100.0</confidence>
+               <clade>
+                  <branch_length>0.22058</branch_length>
+                  <confidence type="unknown">89.0</confidence>
+                  <clade>
+                     <branch_length>0.28901</branch_length>
+                     <confidence type="unknown">100.0</confidence>
+                     <clade>
+                        <branch_length>0.06584</branch_length>
+                        <confidence type="unknown">100.0</confidence>
+                        <clade>
+                           <branch_length>0.02309</branch_length>
+                           <confidence type="unknown">43.0</confidence>
+                           <clade>
+                              <branch_length>0.0746</branch_length>
+                              <confidence type="unknown">100.0</confidence>
+                              <clade>
+                                 <branch_length>0.02365</branch_length>
+                                 <confidence type="unknown">88.0</confidence>
+                                 <clade>
+                                    <name>22_MOUSE</name>
+                                    <branch_length>0.05998</branch_length>
+                                    <taxonomy>
+                                       <code>MOUSE</code>
+                                    </taxonomy>
+                                    <sequence>
+                                       <domain_architecture length="1249">
+                                          <domain from="6" to="90" confidence="7.0E-26">CARD</domain>
+                                          <domain from="109" to="414" confidence="7.2E-117">NB-ARC</domain>
+                                          <domain from="605" to="643" confidence="2.4E-6">WD40</domain>
+                                          <domain from="647" to="685" confidence="1.1E-12">WD40</domain>
+                                          <domain from="689" to="729" confidence="2.4E-7">WD40</domain>
+                                          <domain from="733" to="771" confidence="4.7E-14">WD40</domain>
+                                          <domain from="872" to="910" confidence="2.5E-8">WD40</domain>
+                                          <domain from="993" to="1031" confidence="4.6E-6">WD40</domain>
+                                          <domain from="1075" to="1113" confidence="6.3E-7">WD40</domain>
+                                          <domain from="1117" to="1155" confidence="1.4E-7">WD40</domain>
+                                          <domain from="1168" to="1204" confidence="0.3">WD40</domain>
+                                       </domain_architecture>
+                                    </sequence>
+                                 </clade>
+                                 <clade>
+                                    <name>Apaf-1_HUMAN</name>
+                                    <branch_length>0.01825</branch_length>
+                                    <taxonomy>
+                                       <code>HUMAN</code>
+                                    </taxonomy>
+                                    <sequence>
+                                       <domain_architecture length="1248">
+                                          <domain from="6" to="90" confidence="1.1E-25">CARD</domain>
+                                          <domain from="109" to="414" confidence="3.0E-134">NB-ARC</domain>
+                                          <domain from="605" to="643" confidence="8.5E-6">WD40</domain>
+                                          <domain from="647" to="685" confidence="2.5E-11">WD40</domain>
+                                          <domain from="689" to="729" confidence="2.4E-8">WD40</domain>
+                                          <domain from="733" to="771" confidence="3.6E-14">WD40</domain>
+                                          <domain from="872" to="910" confidence="3.8E-8">WD40</domain>
+                                          <domain from="1075" to="1113" confidence="4.0E-7">WD40</domain>
+                                          <domain from="1117" to="1155" confidence="5.9E-8">WD40</domain>
+                                       </domain_architecture>
+                                    </sequence>
+                                 </clade>
+                              </clade>
+                              <clade>
+                                 <name>12_CANFA</name>
+                                 <branch_length>0.04683</branch_length>
+                                 <taxonomy>
+                                    <code>CANFA</code>
+                                 </taxonomy>
+                                 <sequence>
+                                    <domain_architecture length="1153">
+                                       <domain from="6" to="90" confidence="4.5E-22">CARD</domain>
+                                       <domain from="110" to="415" confidence="4.0E-119">NB-ARC</domain>
+                                       <domain from="597" to="635" confidence="3.9E-5">WD40</domain>
+                                       <domain from="639" to="677" confidence="2.5E-11">WD40</domain>
+                                       <domain from="681" to="721" confidence="1.8E-7">WD40</domain>
+                                       <domain from="725" to="763" confidence="9.4E-13">WD40</domain>
+                                       <domain from="889" to="927" confidence="1.1E-6">WD40</domain>
+                                       <domain from="971" to="1009" confidence="1.7E-7">WD40</domain>
+                                       <domain from="1013" to="1051" confidence="1.9E-7">WD40</domain>
+                                    </domain_architecture>
+                                 </sequence>
+                              </clade>
+                           </clade>
+                           <clade>
+                              <name>11_CHICK</name>
+                              <branch_length>0.15226</branch_length>
+                              <taxonomy>
+                                 <code>CHICK</code>
+                              </taxonomy>
+                              <sequence>
+                                 <domain_architecture length="1207">
+                                    <domain from="6" to="90" confidence="3.6E-21">CARD</domain>
+                                    <domain from="109" to="414" confidence="3.6E-109">NB-ARC</domain>
+                                    <domain from="603" to="641" confidence="1.6E-4">WD40</domain>
+                                    <domain from="645" to="683" confidence="8.2E-11">WD40</domain>
+                                    <domain from="687" to="727" confidence="6.2E-10">WD40</domain>
+                                    <domain from="731" to="769" confidence="1.8E-11">WD40</domain>
+                                    <domain from="828" to="866" confidence="1.8">WD40</domain>
+                                    <domain from="993" to="1030" confidence="2.9E-4">WD40</domain>
+                                    <domain from="1034" to="1072" confidence="1.7E-8">WD40</domain>
+                                    <domain from="1076" to="1114" confidence="7.5E-9">WD40</domain>
+                                    <domain from="1127" to="1163" confidence="0.044">WD40</domain>
+                                 </domain_architecture>
+                              </sequence>
+                           </clade>
+                        </clade>
+                        <clade>
+                           <name>16_XENLA</name>
+                           <branch_length>0.4409</branch_length>
+                           <taxonomy>
+                              <code>XENLA</code>
+                           </taxonomy>
+                           <sequence>
+                              <domain_architecture length="1362">
+                                 <domain from="6" to="90" confidence="4.0E-20">CARD</domain>
+                                 <domain from="109" to="410" confidence="3.1E-56">NB-ARC</domain>
+                                 <domain from="148" to="298" confidence="0.8">NACHT</domain>
+                                 <domain from="729" to="767" confidence="7.0E-6">WD40</domain>
+                                 <domain from="771" to="809" confidence="2.3E-11">WD40</domain>
+                                 <domain from="813" to="853" confidence="1.1E-8">WD40</domain>
+                                 <domain from="857" to="895" confidence="1.1E-10">WD40</domain>
+                                 <domain from="992" to="1030" confidence="8.4E-9">WD40</domain>
+                                 <domain from="1116" to="1154" confidence="7.3E-11">WD40</domain>
+                                 <domain from="1158" to="1196" confidence="1.6E-8">WD40</domain>
+                                 <domain from="1200" to="1238" confidence="1.2E-7">WD40</domain>
+                              </domain_architecture>
+                           </sequence>
+                        </clade>
+                     </clade>
+                     <clade>
+                        <branch_length>0.17031</branch_length>
+                        <confidence type="unknown">100.0</confidence>
+                        <clade>
+                           <branch_length>0.10929</branch_length>
+                           <confidence type="unknown">100.0</confidence>
+                           <clade>
+                              <name>14_FUGRU</name>
+                              <branch_length>0.02255</branch_length>
+                              <taxonomy>
+                                 <code>FUGRU</code>
+                              </taxonomy>
+                              <sequence>
+                                 <domain_architecture length="1258">
+                                    <domain from="8" to="92" confidence="4.6E-24">CARD</domain>
+                                    <domain from="111" to="418" confidence="7.0E-74">NB-ARC</domain>
+                                    <domain from="609" to="647" confidence="2.8E-4">WD40</domain>
+                                    <domain from="651" to="689" confidence="2.3E-12">WD40</domain>
+                                    <domain from="740" to="778" confidence="1.8E-6">WD40</domain>
+                                    <domain from="874" to="912" confidence="1.6E-9">WD40</domain>
+                                    <domain from="998" to="1036" confidence="9.8E-13">WD40</domain>
+                                    <domain from="1040" to="1080" confidence="1.6E-4">WD40</domain>
+                                    <domain from="1084" to="1122" confidence="1.5E-9">WD40</domain>
+                                    <domain from="1126" to="1164" confidence="6.2E-9">WD40</domain>
+                                 </domain_architecture>
+                              </sequence>
+                           </clade>
+                           <clade>
+                              <name>15_TETNG</name>
+                              <branch_length>0.09478</branch_length>
+                              <taxonomy>
+                                 <code>TETNG</code>
+                              </taxonomy>
+                              <sequence>
+                                 <domain_architecture length="621">
+                                    <domain from="8" to="92" confidence="2.5E-24">CARD</domain>
+                                    <domain from="104" to="308" confidence="9.8E-11">NB-ARC</domain>
+                                    <domain from="366" to="404" confidence="1.2E-12">WD40</domain>
+                                    <domain from="455" to="493" confidence="1.0E-10">WD40</domain>
+                                    <domain from="537" to="575" confidence="4.1E-10">WD40</domain>
+                                 </domain_architecture>
+                              </sequence>
+                           </clade>
+                        </clade>
+                        <clade>
+                           <name>17_BRARE</name>
+                           <branch_length>0.1811</branch_length>
+                           <taxonomy>
+                              <code>BRARE</code>
+                           </taxonomy>
+                           <sequence>
+                              <domain_architecture length="1260">
+                                 <domain from="6" to="90" confidence="3.9E-23">CARD</domain>
+                                 <domain from="137" to="444" confidence="1.7E-72">NB-ARC</domain>
+                                 <domain from="635" to="673" confidence="1.6">WD40</domain>
+                                 <domain from="694" to="732" confidence="5.3E-12">WD40</domain>
+                                 <domain from="783" to="821" confidence="2.0E-8">WD40</domain>
+                                 <domain from="1040" to="1078" confidence="2.4E-8">WD40</domain>
+                                 <domain from="1081" to="1121" confidence="6.6E-4">WD40</domain>
+                                 <domain from="1125" to="1163" confidence="5.1E-8">WD40</domain>
+                                 <domain from="1167" to="1205" confidence="1.3E-7">WD40</domain>
+                              </domain_architecture>
+                           </sequence>
+                        </clade>
+                     </clade>
+                  </clade>
+                  <clade>
+                     <branch_length>0.01594</branch_length>
+                     <confidence type="unknown">53.0</confidence>
+                     <clade>
+                        <branch_length>0.10709</branch_length>
+                        <confidence type="unknown">68.0</confidence>
+                        <clade>
+                           <name>1_BRAFL</name>
+                           <branch_length>0.26131</branch_length>
+                           <taxonomy>
+                              <code>BRAFL</code>
+                           </taxonomy>
+                           <sequence>
+                              <domain_architecture length="1238">
+                                 <domain from="6" to="89" confidence="5.7E-19">CARD</domain>
+                                 <domain from="111" to="413" confidence="4.2E-48">NB-ARC</domain>
+                                 <domain from="600" to="638" confidence="3.2E-8">WD40</domain>
+                                 <domain from="642" to="680" confidence="1.5E-10">WD40</domain>
+                                 <domain from="730" to="768" confidence="9.6E-11">WD40</domain>
+                                 <domain from="857" to="895" confidence="3.7E-10">WD40</domain>
+                                 <domain from="984" to="1022" confidence="6.7E-10">WD40</domain>
+                                 <domain from="1025" to="1064" confidence="3.1E-6">WD40</domain>
+                                 <domain from="1069" to="1107" confidence="1.5E-4">WD40</domain>
+                                 <domain from="1111" to="1149" confidence="7.9E-7">WD40</domain>
+                              </domain_architecture>
+                           </sequence>
+                        </clade>
+                        <clade>
+                           <name>18_NEMVE</name>
+                           <branch_length>0.38014</branch_length>
+                           <taxonomy>
+                              <code>NEMVE</code>
+                           </taxonomy>
+                           <sequence>
+                              <domain_architecture length="1290">
+                                 <domain from="7" to="90" confidence="1.5E-13">CARD</domain>
+                                 <domain from="117" to="200" confidence="5.4E-14">CARD</domain>
+                                 <domain from="216" to="517" confidence="1.5E-50">NB-ARC</domain>
+                                 <domain from="711" to="749" confidence="1.0E-7">WD40</domain>
+                                 <domain from="753" to="791" confidence="8.5E-12">WD40</domain>
+                                 <domain from="795" to="833" confidence="4.3E-11">WD40</domain>
+                                 <domain from="837" to="875" confidence="1.0E-12">WD40</domain>
+                                 <domain from="920" to="957" confidence="2.0E-4">WD40</domain>
+                                 <domain from="961" to="999" confidence="3.0E-6">WD40</domain>
+                                 <domain from="1085" to="1123" confidence="4.4E-6">WD40</domain>
+                                 <domain from="1128" to="1166" confidence="3.0E-4">WD40</domain>
+                                 <domain from="1170" to="1207" confidence="1.7E-10">WD40</domain>
+                              </domain_architecture>
+                           </sequence>
+                        </clade>
+                     </clade>
+                     <clade>
+                        <name>23_STRPU</name>
+                        <branch_length>0.48179</branch_length>
+                        <taxonomy>
+                           <code>STRPU</code>
+                        </taxonomy>
+                        <sequence>
+                           <domain_architecture length="1236">
+                              <domain from="110" to="402" confidence="1.0E-40">NB-ARC</domain>
+                              <domain from="594" to="632" confidence="8.9E-4">WD40</domain>
+                              <domain from="636" to="673" confidence="2.5E-6">WD40</domain>
+                              <domain from="721" to="759" confidence="0.0043">WD40</domain>
+                              <domain from="765" to="802" confidence="0.0036">WD40</domain>
+                              <domain from="848" to="886" confidence="9.0E-10">WD40</domain>
+                              <domain from="975" to="1013" confidence="1.9E-5">WD40</domain>
+                              <domain from="1015" to="1053" confidence="2.4E-6">WD40</domain>
+                              <domain from="1057" to="1095" confidence="2.7E-9">WD40</domain>
+                              <domain from="1099" to="1137" confidence="4.9E-8">WD40</domain>
+                              <domain from="1141" to="1177" confidence="0.011">WD40</domain>
+                           </domain_architecture>
+                        </sequence>
+                     </clade>
+                  </clade>
+               </clade>
+               <clade>
+                  <branch_length>0.34475</branch_length>
+                  <confidence type="unknown">100.0</confidence>
+                  <clade>
+                     <name>26_STRPU</name>
+                     <branch_length>0.36374</branch_length>
+                     <taxonomy>
+                        <code>STRPU</code>
+                     </taxonomy>
+                     <sequence>
+                        <domain_architecture length="1319">
+                           <domain from="18" to="98" confidence="3.4E-5">Death</domain>
+                           <domain from="189" to="481" confidence="1.8E-10">NB-ARC</domain>
+                           <domain from="630" to="668" confidence="8.2E-5">WD40</domain>
+                        </domain_architecture>
+                     </sequence>
+                  </clade>
+                  <clade>
+                     <name>25_STRPU</name>
+                     <branch_length>0.33137</branch_length>
+                     <taxonomy>
+                        <code>STRPU</code>
+                     </taxonomy>
+                     <sequence>
+                        <domain_architecture length="1947">
+                           <domain from="143" to="227" confidence="7.4E-5">Death</domain>
+                           <domain from="227" to="550" confidence="2.0E-13">NB-ARC</domain>
+                           <domain from="697" to="736" confidence="7.9E-4">WD40</domain>
+                           <domain from="745" to="785" confidence="1.5">WD40</domain>
+                           <domain from="1741" to="1836" confidence="2.0">Adeno_VII</domain>
+                        </domain_architecture>
+                     </sequence>
+                  </clade>
+               </clade>
+            </clade>
+            <clade>
+               <branch_length>1.31498</branch_length>
+               <confidence type="unknown">100.0</confidence>
+               <clade>
+                  <name>CED4_CAEEL</name>
+                  <branch_length>0.13241</branch_length>
+                  <taxonomy>
+                     <code>CAEEL</code>
+                  </taxonomy>
+                  <sequence>
+                     <domain_architecture length="714">
+                        <domain from="7" to="90" confidence="9.2E-14">CARD</domain>
+                        <domain from="116" to="442" confidence="5.8E-151">NB-ARC</domain>
+                     </domain_architecture>
+                  </sequence>
+               </clade>
+               <clade>
+                  <name>31_CAEBR</name>
+                  <branch_length>0.04777</branch_length>
+                  <taxonomy>
+                     <code>CAEBR</code>
+                  </taxonomy>
+                  <sequence>
+                     <domain_architecture length="554">
+                        <domain from="1" to="75" confidence="0.0046">CARD</domain>
+                        <domain from="101" to="427" confidence="2.1E-123">NB-ARC</domain>
+                     </domain_architecture>
+                  </sequence>
+               </clade>
+            </clade>
+         </clade>
+         <clade>
+            <branch_length>0.13172</branch_length>
+            <confidence type="unknown">45.0</confidence>
+            <clade>
+               <branch_length>0.24915</branch_length>
+               <confidence type="unknown">95.0</confidence>
+               <clade>
+                  <branch_length>0.76898</branch_length>
+                  <confidence type="unknown">100.0</confidence>
+                  <clade>
+                     <name>28_DROPS</name>
+                     <branch_length>0.1732</branch_length>
+                     <taxonomy>
+                        <code>DROPS</code>
+                     </taxonomy>
+                     <sequence>
+                        <domain_architecture length="535">
+                           <domain from="112" to="399" confidence="1.4E-5">NB-ARC</domain>
+                        </domain_architecture>
+                     </sequence>
+                  </clade>
+                  <clade>
+                     <name>Dark_DROME</name>
+                     <branch_length>0.18863</branch_length>
+                     <taxonomy>
+                        <code>DROME</code>
+                     </taxonomy>
+                     <sequence>
+                        <domain_architecture length="1421">
+                           <domain from="108" to="397" confidence="2.1E-5">NB-ARC</domain>
+                        </domain_architecture>
+                     </sequence>
+                  </clade>
+               </clade>
+               <clade>
+                  <name>29_AEDAE</name>
+                  <branch_length>0.86398</branch_length>
+                  <taxonomy>
+                     <code>AEDAE</code>
+                  </taxonomy>
+                  <sequence>
+                     <domain_architecture length="423">
+                        <domain from="109" to="421" confidence="9.3E-6">NB-ARC</domain>
+                     </domain_architecture>
+                  </sequence>
+               </clade>
+            </clade>
+            <clade>
+               <name>30_TRICA</name>
+               <branch_length>0.97698</branch_length>
+               <taxonomy>
+                  <code>TRICA</code>
+               </taxonomy>
+               <sequence>
+                  <domain_architecture length="1279">
+                     <domain from="5" to="81" confidence="0.59">CARD</domain>
+                     <domain from="92" to="400" confidence="9.0E-11">NB-ARC</domain>
+                     <domain from="630" to="668" confidence="1.1E-5">WD40</domain>
+                  </domain_architecture>
+               </sequence>
+            </clade>
+         </clade>
+      </clade>
+      <clade>
+         <branch_length>0.18105</branch_length>
+         <confidence type="unknown">89.0</confidence>
+         <clade>
+            <branch_length>0.15891</branch_length>
+            <confidence type="unknown">64.0</confidence>
+            <clade>
+               <branch_length>0.54836</branch_length>
+               <confidence type="unknown">100.0</confidence>
+               <clade>
+                  <branch_length>0.09305</branch_length>
+                  <confidence type="unknown">46.0</confidence>
+                  <clade>
+                     <branch_length>0.21648</branch_length>
+                     <confidence type="unknown">61.0</confidence>
+                     <clade>
+                        <branch_length>0.93134</branch_length>
+                        <confidence type="unknown">100.0</confidence>
+                        <clade>
+                           <name>34_BRAFL</name>
+                           <branch_length>0.093</branch_length>
+                           <taxonomy>
+                              <code>BRAFL</code>
+                           </taxonomy>
+                           <sequence>
+                              <domain_architecture length="752">
+                                 <domain from="49" to="356" confidence="9.0E-6">NB-ARC</domain>
+                              </domain_architecture>
+                           </sequence>
+                        </clade>
+                        <clade>
+                           <name>35_BRAFL</name>
+                           <branch_length>0.08226</branch_length>
+                           <taxonomy>
+                              <code>BRAFL</code>
+                           </taxonomy>
+                           <sequence>
+                              <domain_architecture length="753">
+                                 <domain from="25" to="105" confidence="0.16">DED</domain>
+                                 <domain from="113" to="409" confidence="1.1E-6">NB-ARC</domain>
+                              </domain_architecture>
+                           </sequence>
+                        </clade>
+                     </clade>
+                     <clade>
+                        <name>8_BRAFL</name>
+                        <branch_length>0.58563</branch_length>
+                        <taxonomy>
+                           <code>BRAFL</code>
+                        </taxonomy>
+                        <sequence>
+                           <domain_architecture length="916">
+                              <domain from="58" to="369" confidence="8.4E-7">NB-ARC</domain>
+                           </domain_architecture>
+                        </sequence>
+                     </clade>
+                  </clade>
+                  <clade>
+                     <branch_length>0.28437</branch_length>
+                     <confidence type="unknown">84.0</confidence>
+                     <clade>
+                        <name>20_NEMVE</name>
+                        <branch_length>0.71946</branch_length>
+                        <taxonomy>
+                           <code>NEMVE</code>
+                        </taxonomy>
+                        <sequence>
+                           <domain_architecture length="786">
+                              <domain from="8" to="91" confidence="1.7E-17">DED</domain>
+                              <domain from="8" to="85" confidence="0.37">PAAD_DAPIN</domain>
+                              <domain from="90" to="388" confidence="6.8E-5">NB-ARC</domain>
+                              <domain from="575" to="608" confidence="0.27">TPR_1</domain>
+                              <domain from="657" to="690" confidence="0.22">TPR_2</domain>
+                              <domain from="698" to="731" confidence="4.2E-5">TPR_2</domain>
+                           </domain_architecture>
+                        </sequence>
+                     </clade>
+                     <clade>
+                        <name>21_NEMVE</name>
+                        <branch_length>0.9571</branch_length>
+                        <taxonomy>
+                           <code>NEMVE</code>
+                        </taxonomy>
+                        <sequence>
+                           <domain_architecture length="1563">
+                              <domain from="234" to="317" confidence="2.3E-14">CARD</domain>
+                              <domain from="238" to="318" confidence="0.5">Death</domain>
+                              <domain from="329" to="619" confidence="0.022">NB-ARC</domain>
+                              <domain from="906" to="939" confidence="0.17">TPR_1</domain>
+                              <domain from="1326" to="1555" confidence="3.2E-26">RVT_1</domain>
+                           </domain_architecture>
+                        </sequence>
+                     </clade>
+                  </clade>
+               </clade>
+               <clade>
+                  <name>9_BRAFL</name>
+                  <branch_length>1.09612</branch_length>
+                  <taxonomy>
+                     <code>BRAFL</code>
+                  </taxonomy>
+                  <sequence>
+                     <domain_architecture length="1011">
+                        <domain from="5" to="321" confidence="5.0E-5">NB-ARC</domain>
+                        <domain from="497" to="616" confidence="1.6">BTAD</domain>
+                        <domain from="500" to="533" confidence="5.6E-4">TPR_1</domain>
+                        <domain from="542" to="575" confidence="0.43">TPR_1</domain>
+                        <domain from="626" to="659" confidence="0.0084">TPR_2</domain>
+                        <domain from="708" to="741" confidence="1.9E-4">TPR_2</domain>
+                        <domain from="708" to="739" confidence="1.3">TPR_3</domain>
+                        <domain from="708" to="733" confidence="0.16">TPR_4</domain>
+                        <domain from="833" to="916" confidence="5.6E-14">Death</domain>
+                        <domain from="846" to="868" confidence="0.36">LTXXQ</domain>
+                        <domain from="930" to="1011" confidence="8.3E-17">Death</domain>
+                     </domain_architecture>
+                  </sequence>
+               </clade>
+            </clade>
+            <clade>
+               <branch_length>0.34914</branch_length>
+               <confidence type="unknown">98.0</confidence>
+               <clade>
+                  <branch_length>0.22189</branch_length>
+                  <confidence type="unknown">95.0</confidence>
+                  <clade>
+                     <name>3_BRAFL</name>
+                     <branch_length>0.48766</branch_length>
+                     <taxonomy>
+                        <code>BRAFL</code>
+                     </taxonomy>
+                     <sequence>
+                        <domain_architecture length="2080">
+                           <domain from="116" to="423" confidence="1.4E-12">NB-ARC</domain>
+                           <domain from="620" to="659" confidence="1.4E-6">WD40</domain>
+                           <domain from="663" to="701" confidence="1.4E-8">WD40</domain>
+                           <domain from="705" to="743" confidence="3.0E-11">WD40</domain>
+                           <domain from="747" to="785" confidence="1.1E-8">WD40</domain>
+                           <domain from="788" to="826" confidence="1.6E-5">WD40</domain>
+                           <domain from="830" to="870" confidence="1.3E-4">WD40</domain>
+                           <domain from="874" to="914" confidence="6.2E-9">WD40</domain>
+                           <domain from="919" to="957" confidence="0.0011">WD40</domain>
+                           <domain from="961" to="1000" confidence="1.8E-8">WD40</domain>
+                           <domain from="1013" to="1051" confidence="1.3E-6">WD40</domain>
+                           <domain from="1055" to="1092" confidence="0.096">WD40</domain>
+                           <domain from="1794" to="1853" confidence="3.6E-4">Collagen</domain>
+                        </domain_architecture>
+                     </sequence>
+                  </clade>
+                  <clade>
+                     <name>2_BRAFL</name>
+                     <branch_length>0.65293</branch_length>
+                     <taxonomy>
+                        <code>BRAFL</code>
+                     </taxonomy>
+                     <sequence>
+                        <domain_architecture length="1691">
+                           <domain from="162" to="457" confidence="4.4E-10">NB-ARC</domain>
+                           <domain from="640" to="680" confidence="0.0068">WD40</domain>
+                           <domain from="684" to="722" confidence="1.6E-8">WD40</domain>
+                           <domain from="726" to="764" confidence="6.0E-9">WD40</domain>
+                           <domain from="827" to="865" confidence="6.9E-10">WD40</domain>
+                           <domain from="868" to="906" confidence="1.2E-6">WD40</domain>
+                           <domain from="910" to="950" confidence="0.0080">WD40</domain>
+                           <domain from="954" to="994" confidence="0.0016">WD40</domain>
+                           <domain from="999" to="1037" confidence="4.9E-6">WD40</domain>
+                           <domain from="1042" to="1080" confidence="6.3E-8">WD40</domain>
+                           <domain from="1100" to="1138" confidence="1.9E-8">WD40</domain>
+                           <domain from="1142" to="1178" confidence="1.4">WD40</domain>
+                           <domain from="1577" to="1615" confidence="4.3E-4">WD40</domain>
+                        </domain_architecture>
+                     </sequence>
+                  </clade>
+               </clade>
+               <clade>
+                  <name>19_NEMVE</name>
+                  <branch_length>0.57144</branch_length>
+                  <taxonomy>
+                     <code>NEMVE</code>
+                  </taxonomy>
+                  <sequence>
+                     <domain_architecture length="1649">
+                        <domain from="99" to="174" confidence="4.6E-7">DED</domain>
+                        <domain from="181" to="503" confidence="8.0E-13">NB-ARC</domain>
+                        <domain from="696" to="734" confidence="1.4E-8">WD40</domain>
+                        <domain from="738" to="776" confidence="2.9E-9">WD40</domain>
+                        <domain from="780" to="818" confidence="3.8E-10">WD40</domain>
+                        <domain from="822" to="860" confidence="6.4E-9">WD40</domain>
+                        <domain from="864" to="902" confidence="2.1E-10">WD40</domain>
+                        <domain from="906" to="944" confidence="1.3E-8">WD40</domain>
+                        <domain from="948" to="986" confidence="1.2E-8">WD40</domain>
+                        <domain from="990" to="1028" confidence="9.4E-8">WD40</domain>
+                        <domain from="1032" to="1070" confidence="6.0E-8">WD40</domain>
+                        <domain from="1074" to="1112" confidence="2.6E-4">WD40</domain>
+                        <domain from="1364" to="1597" confidence="1.9">SGL</domain>
+                        <domain from="1442" to="1480" confidence="9.7E-7">WD40</domain>
+                        <domain from="1527" to="1565" confidence="1.2">WD40</domain>
+                        <domain from="1568" to="1606" confidence="1.1E-6">WD40</domain>
+                     </domain_architecture>
+                  </sequence>
+               </clade>
+            </clade>
+         </clade>
+         <clade>
+            <branch_length>0.43438</branch_length>
+            <confidence type="unknown">92.0</confidence>
+            <clade>
+               <branch_length>0.92214</branch_length>
+               <confidence type="unknown">100.0</confidence>
+               <clade>
+                  <name>37_BRAFL</name>
+                  <branch_length>0.21133</branch_length>
+                  <taxonomy>
+                     <code>BRAFL</code>
+                  </taxonomy>
+                  <sequence>
+                     <domain_architecture length="1793">
+                        <domain from="6" to="89" confidence="9.6E-13">CARD</domain>
+                        <domain from="118" to="202" confidence="4.5E-9">CARD</domain>
+                        <domain from="206" to="491" confidence="0.0011">NB-ARC</domain>
+                        <domain from="238" to="388" confidence="0.0043">NACHT</domain>
+                     </domain_architecture>
+                  </sequence>
+               </clade>
+               <clade>
+                  <name>36_BRAFL</name>
+                  <branch_length>0.16225</branch_length>
+                  <taxonomy>
+                     <code>BRAFL</code>
+                  </taxonomy>
+                  <sequence>
+                     <domain_architecture length="918">
+                        <domain from="9" to="93" confidence="1.6E-9">CARD</domain>
+                        <domain from="98" to="403" confidence="0.0019">NB-ARC</domain>
+                     </domain_architecture>
+                  </sequence>
+               </clade>
+            </clade>
+            <clade>
+               <name>33_BRAFL</name>
+               <branch_length>0.8363</branch_length>
+               <taxonomy>
+                  <code>BRAFL</code>
+               </taxonomy>
+               <sequence>
+                  <domain_architecture length="1212">
+                     <domain from="5" to="87" confidence="4.7E-12">Death</domain>
+                     <domain from="154" to="465" confidence="2.0E-6">NB-ARC</domain>
+                  </domain_architecture>
+               </sequence>
+            </clade>
+         </clade>
+      </clade>
+   </clade>
+</phylogeny>
+</phyloxml>