1 <?xml version="1.0" encoding="UTF-8"?>
2 <phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd" xmlns="http://www.phyloxml.org">
3 <phylogeny rooted="true" rerootable="false">
5 <name>cellular_organisms</name>
13 <name>Opisthokonta</name>
15 <name>Metazoa_Choanoflagellata</name>
18 <reference doi="10.1038/nature06614">
21 <name>Bilateria_Cnidaria</name>
23 <name>Bilateria</name>
25 <name>Deuterostomia</name>
26 <reference doi="10.1038/nature04336">
31 <name>Urochordata_Vertebrata</name>
33 <name>Vertebrata</name>
35 <name>Tetrapoda</name>
39 <id provider="tol">14990</id>
40 <scientific_name>Amniota</scientific_name>
49 <name>Euarchontoglires</name>
84 <id provider="tol">14866</id>
85 <scientific_name>Diapsida</scientific_name>
88 <name>Neognathae</name>
90 <id provider="uniprot">8825</id>
91 <scientific_name>Neognathae</scientific_name>
92 <rank>superorder</rank>
97 <id provider="eol">10199408</id>
99 <scientific_name>Gallus gallus</scientific_name>
100 <common_name>Chicken</common_name>
101 <synonym>Gallus domesticus</synonym>
107 <id provider="uniprot">59729</id>
109 <scientific_name>Taeniopygia guttata</scientific_name>
110 <common_name>Zebra finch</common_name>
111 <synonym>Poephila guttata</synonym>
119 <id provider="eol">795869</id>
121 <scientific_name>Anolis carolinensis</scientific_name>
122 <authority>Voigt, 1832</authority>
123 <common_name>Green anole</common_name>
124 <synonym>American chameleon</synonym>
135 <name>Teleostei</name>
137 <name>Euteleostei</name>
139 <name>Smegmamorpha</name>
141 <id provider="ncbi">129949</id>
151 <name>Tetraodontiformes</name>
166 <name>Urochordata</name>
168 <id provider="ncbi">7712</id>
169 <scientific_name>Urochordata</scientific_name>
170 <common_name>tunicates</common_name>
173 <name>Ascidiacea</name>
175 <id provider="ncbi">7713</id>
176 <scientific_name>Ascidiacea</scientific_name>
177 <common_name>sea squirts</common_name>
189 <id provider="ncbi">34765</id>
190 <scientific_name>Oikopleura dioica</scientific_name>
204 <name>Protostomia</name>
206 <name>Ecdysozoa</name>
208 <name>Arthropoda</name>
212 <name>Neoptera</name>
214 <id provider="tol">8267</id>
215 <scientific_name>Neoptera</scientific_name>
216 <rank>subclass</rank>
219 <name>Endopterygota</name>
221 <id provider="eol">3016961</id>
222 <scientific_name>Endopterygota</scientific_name>
223 <synonym>Holometabola</synonym>
224 <rank>infraclass</rank>
225 <uri>http://tolweb.org/Endopterygota/</uri>
228 <name>Lepidoptera_Diptera</name>
232 <name>Culicoidea</name>
244 <name>Muscomorpha</name>
258 <name>Hymenoptera</name>
270 <id provider="uniprot">7029</id>
272 <scientific_name>Acyrthosiphon pisum</scientific_name>
273 <common_name>Pea aphid</common_name>
274 <synonym>Acyrhosiphum pisum</synonym>
288 <name>Nematoda</name>
290 <id provider="tol">2472</id>
291 <scientific_name>Nematoda</scientific_name>
293 <reference doi="10.1038/32160">
296 <name>nematode Clade V</name>
298 <name>Caenorhabditis</name>
300 <scientific_name>Caenorhabditis</scientific_name>
325 <name>Lophotrochozoa</name>
327 <name>Annelida_Mollusca</name>
329 <name>Annelida</name>
342 <name>Platyhelminthes</name>
354 <name>Cnidaria</name>
356 <id provider="uniprot">6073</id>
357 <scientific_name>Cnidaria</scientific_name>
365 <id provider="eol">9119928</id>
367 <scientific_name>Hydra magnipapillata</scientific_name>
368 <authority>Ito, 1947</authority>
370 <uri>http://www.nig.ac.jp/labs/OntoGen/magni.html</uri>
377 <reference doi="10.1073/pnas.0602076103">
388 <name>Dikarya_Mucoromycotina_Chytridiomycota</name>
390 <name>Dikarya_Mucoromycotina</name>
394 <id provider="uniprot">451864</id>
395 <scientific_name>Dikarya</scientific_name>
398 <name>Ascomycota</name>
400 <name>Pezizomycotina</name>
402 <id provider="uniprot">147538</id>
403 <scientific_name>Pezizomycotina</scientific_name>
404 <synonym>Euascomycota</synonym>
405 <rank>subphylum</rank>
408 <name>Sordariomycetes_Dothideomycetes_Eurotiales</name>
410 <name>Sordariomycetes_Dothideomycetes</name>
412 <name>Sordariomycetes</name>
414 <id provider="uniprot">147550</id>
415 <scientific_name>Sordariomycetes</scientific_name>
416 <synonym>Pyrenomycetes</synonym>
420 <name>Magnaporthales_Hypocreales</name>
422 <name>Hypocreales</name>
424 <id provider="uniprot">5125</id>
425 <scientific_name>Hypocreales</scientific_name>
426 <synonym>pyrenomycetes</synonym>
441 <name>Sordariales</name>
443 <id provider="uniprot">5139</id>
444 <scientific_name>Sordariales</scientific_name>
445 <synonym>pyrenonmycetes</synonym>
449 <name>Chaetomiaceae</name>
451 <id provider="uniprot">35718</id>
452 <scientific_name>Chaetomiaceae</scientific_name>
458 <id provider="eol">1029505</id>
460 <scientific_name>Chaetomium globosum</scientific_name>
461 <authority>Kunze 1817</authority>
462 <common_name>Soil fungus</common_name>
469 <id provider="eol">193532</id>
471 <scientific_name>Thielavia terrestris</scientific_name>
472 <authority>Malloch & Cain 1972</authority>
473 <synonym>Acremonium alabamense</synonym>
484 <name>Dothideomycetes</name>
486 <id provider="uniprot">147541</id>
487 <scientific_name>Dothideomycetes</scientific_name>
488 <synonym>Loculoascomycetes</synonym>
489 <synonym>bitunicate ascomycetes</synonym>
493 <name>Pleosporales</name>
495 <id provider="uniprot">92860</id>
496 <scientific_name>Pleosporales</scientific_name>
497 <synonym>Melanommatales</synonym>
501 <name>Pleosporaceae</name>
503 <id provider="uniprot">28556</id>
504 <scientific_name>Pleosporaceae</scientific_name>
505 <synonym>Pyrenophoraceae</synonym>
520 <name>Mycosphaerella</name>
522 <id provider="uniprot">41254</id>
523 <scientific_name>Mycosphaerella</scientific_name>
536 <name>Eurotiales</name>
538 <id provider="uniprot">5042</id>
539 <scientific_name>Eurotiales</scientific_name>
540 <common_name>green and blue molds</common_name>
541 <synonym>Elaphomycetales</synonym>
545 <name>Neosartorya_Emericella</name>
552 <id provider="eol">195546</id>
554 <scientific_name>Emericella nidulans</scientific_name>
555 <authority>Vuill. 1927</authority>
556 <synonym>Aspergillus nidulans</synonym>
562 <name>Aspergillus</name>
564 <id provider="uniprot">5052</id>
565 <scientific_name>Aspergillus</scientific_name>
577 <name>Onygenales</name>
579 <id provider="uniprot">33183</id>
580 <scientific_name>Onygenales</scientific_name>
581 <synonym>Gymnoascales</synonym>
593 <name>Saccharomycotina_Taphrinomycotina</name>
595 <name>Saccharomycotina</name>
597 <scientific_name>Saccharomycotina</scientific_name>
598 <rank>subphylum</rank>
601 <name>Saccharomycetaceae</name>
603 <id provider="uniprot">4893</id>
604 <scientific_name>Saccharomycetaceae</scientific_name>
618 <name>Taphrinomycotina</name>
629 <name>Basidiomycota</name>
631 <id provider="uniprot">5204</id>
632 <scientific_name>Basidiomycota</scientific_name>
636 <name>Pucciniomycotina_Agaricomycotina</name>
638 <name>Agaricomycotina</name>
640 <id provider="uniprot">5302</id>
641 <scientific_name>Agaricomycotina</scientific_name>
644 <name>Homobasidiomycetes</name>
646 <id provider="uniprot">155619</id>
647 <scientific_name>Homobasidiomycetes</scientific_name>
650 <name>Agaricales</name>
652 <id provider="uniprot">5338</id>
653 <scientific_name>Agaricales</scientific_name>
665 <id provider="uniprot">5322</id>
667 <scientific_name>Pleurotus ostreatus</scientific_name>
668 <common_name>Oyster mushroom</common_name>
676 <id provider="uniprot">104341</id>
677 <scientific_name>Postia placenta</scientific_name>
682 <name>Tremellomycetes</name>
684 <id provider="uniprot">155616</id>
685 <scientific_name>Tremellomycetes</scientific_name>
694 <id provider="eol">1029985</id>
696 <scientific_name>Tremella mesenterica</scientific_name>
697 <authority>Pers. 1800</authority>
698 <common_name>Jelly fungus</common_name>
699 <synonym>Yellow Brain</synonym>
700 <synonym>Tremella lutescens</synonym>
707 <name>Pucciniomycotina</name>
709 <id provider="uniprot">29000</id>
710 <scientific_name>Pucciniomycotina</scientific_name>
711 <synonym>Urediniomycetes</synonym>
712 <rank>subphylum</rank>
715 <name>Pucciniomycetes</name>
717 <id provider="uniprot">162484</id>
718 <scientific_name>Pucciniomycetes</scientific_name>
719 <synonym>Urediniomycetidae</synonym>
720 <rank>subclass</rank>
725 <id provider="eol">1029947</id>
727 <scientific_name>Puccinia graminis</scientific_name>
728 <authority>Pers. 1794</authority>
729 <common_name>Black stem rust fungus</common_name>
730 <synonym>Wheat rust</synonym>
737 <id provider="eol">156696</id>
739 <scientific_name>Melampsora laricis-populina</scientific_name>
740 <authority>Kleb. 1902</authority>
741 <synonym>Melampsora larici-populina</synonym>
742 <synonym>Melampsora laricipopulina</synonym>
750 <id provider="eol">1013696</id>
751 <scientific_name>Sporobolomyces roseus</scientific_name>
752 <authority>Kluyver & C. B. Niel 1924</authority>
764 <name>Mucoromycotina</name>
766 <id provider="uniprot">451507</id>
767 <scientific_name>Mucoromycotina</scientific_name>
768 <synonym>Zygomycota</synonym>
769 <rank>subphylum</rank>
774 <id provider="uniprot">36080</id>
776 <scientific_name>Mucor circinelloides</scientific_name>
777 <synonym>Mucor griseo-roseus</synonym>
799 <name>Amoebozoa</name>
801 <name>Dictyostelium</name>
816 <reference doi="10.1099/ijs.0.63216-0">
819 <name>Corticata</name>
821 <name>Archaeplastida</name>
823 <name>Viridiplantae</name>
825 <name>Embryophyta</name>
827 <name>Tracheophyta</name>
829 <name>Magnoliophyta</name>
831 <name>core eudicotyledons</name>
833 <id provider="uniprot">91827</id>
834 <scientific_name>core eudicotyledons</scientific_name>
835 <synonym>core eudicots</synonym>
836 <uri>http://tolweb.org/Core_Eudicots/20714</uri>
839 <name>Rosids_Vitaceae</name>
843 <id provider="uniprot">71275</id>
844 <scientific_name>rosids</scientific_name>
845 <synonym>Rosidae</synonym>
846 <rank>subclass</rank>
847 <uri>http://tolweb.org/Rosids/20701</uri>
852 <id provider="uniprot">91835</id>
853 <scientific_name>fabids</scientific_name>
854 <synonym>eurosids I</synonym>
855 <uri>http://tolweb.org/Rosids/20701</uri>
858 <name>Malpighiales</name>
860 <id provider="uniprot">3646</id>
861 <scientific_name>Malpighiales</scientific_name>
862 <synonym>Balanopales</synonym>
871 <id provider="uniprot">3983</id>
873 <scientific_name>Manihot esculenta</scientific_name>
874 <common_name>Tapioca</common_name>
880 <name>Fabales_Cucurbitales</name>
884 <id provider="uniprot">3847</id>
886 <scientific_name>Glycine max</scientific_name>
887 <authority>cv. Wye</authority>
888 <common_name>Soybean</common_name>
894 <id provider="uniprot">3659</id>
896 <scientific_name>Cucumis sativus</scientific_name>
897 <common_name>Cucumber</common_name>
904 <name>Arabidopsis</name>
916 <id provider="eol">582304</id>
918 <scientific_name>Vitis vinifera</scientific_name>
925 <id provider="uniprot">4155</id>
927 <scientific_name>Mimulus guttatus</scientific_name>
928 <common_name>Yellow monkey flower</common_name>
958 <name>Chlorophyta</name>
960 <name>Prasinophyceae</name>
962 <name>Ostreococcus</name>
974 <name>Micromonas</name>
984 <name>Trebouxiophyceae_Chlorophyceae</name>
986 <name>Chlorophyceae</name>
997 <id provider="uniprot">310507</id>
999 <scientific_name>Chlorella sp. NC64A</scientific_name>
1008 <id provider="uniprot">45157</id>
1010 <scientific_name>Cyanidioschyzon merolae</scientific_name>
1011 <common_name>Red alga</common_name>
1012 <rank>species</rank>
1013 <uri>http://merolae.biol.s.u-tokyo.ac.jp/</uri>
1018 <name>Chromalveolate</name>
1019 <reference doi="10.1073/pnas.0712248105">
1022 <name>Heterokonta_Alveolata</name>
1024 <name>Alveolata</name>
1026 <name>Apicomplexa</name>
1028 <name>Aconoidasida</name>
1030 <name>Plasmodium</name>
1042 <name>Theileria</name>
1052 <name>Coccidia</name>
1054 <name>Cryptosporidium</name>
1068 <name>Ciliophora</name>
1078 <name>Heterokonta</name>
1080 <scientific_name>Heterokonta</scientific_name>
1081 <common_name>Stramenophiles</common_name>
1084 <name>Pelagophyceae_Bacillariophyta</name>
1086 <name>Bacillariophyta</name>
1088 <scientific_name>Bacillariophyta</scientific_name>
1089 <common_name>Diatoms</common_name>
1093 <name>Bacillariophycidae</name>
1095 <id provider="uniprot">33850</id>
1096 <scientific_name>Bacillariophycidae</scientific_name>
1101 <id provider="eol">912693</id>
1103 <scientific_name>Phaeodactylum tricornutum</scientific_name>
1104 <authority>Bohlin</authority>
1105 <rank>species</rank>
1111 <id provider="eol">911694</id>
1113 <scientific_name>Fragilariopsis cylindrus</scientific_name>
1114 <authority>Krieger</authority>
1115 <synonym>Nitzschia cylindrus</synonym>
1116 <rank>species</rank>
1123 <id provider="eol">916868</id>
1125 <scientific_name>Thalassiosira pseudonana</scientific_name>
1126 <authority>Hasle & Heimdal</authority>
1127 <common_name>Marine diatom</common_name>
1128 <rank>species</rank>
1135 <id provider="eol">912461</id>
1137 <scientific_name>Aureococcus anophagefferens</scientific_name>
1138 <authority>Hargraves & Sieburth</authority>
1139 <rank>species</rank>
1144 <name>Oomycetes</name>
1146 <scientific_name>Oomycetes</scientific_name>
1147 <common_name>water molds</common_name>
1167 <name>Excavata</name>
1168 <reference doi="10.1038/nature04546">
1171 <name>Kinetoplastida_Heterolobosea</name>
1173 <name>Kinetoplastida</name>
1186 <name>Metamonada</name>
1198 <name>Archaea</name>
1484 <name>Bacteria</name>
2138 <name>Clostridia</name>
2140 <id provider="uniprot">186801</id>
2141 <scientific_name>Clostridia</scientific_name>