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Species trees
Species trees can be constructed by several methods. We found that best trees according to biological classifications are the PAM distance trees, where the distances are determined by the average PAM distance between every pair of species. The optimal set of OMA groups from which the distance averages are calculated is based on the "dimensionless fitting index". This is a normalized measure of how well a set of distance estimates can be fit on a tree.
As we process new genome databases the following trees are updated permanentely.
Tree of Archaea
Tree info: All Archaeal genomes, Mon Dec 12 17:36:17 2011, 93 species, 25553 orthologs, 33 top groups, 123 used here, Weighted, BestSubsetDimlessQual: best: 0.8214, ave: 0.9904 +- 0.0051, var: 0.006658, Z=-2.072
Downloads: Unrooted tree (pdf), phylogram (pdf), Newick tree file, PhyloXML tree file or a Darwin script to plot your own tree.
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Color code: Crenarchaeota Methanomicrobia Halobacteria Methanococcaceae Thermococci Methanocaldococcaceae Methanobacteria Archaeoglobi Thermoplasmata Aciduliprofundum Methanopyri environmental samples Korarchaeota Nanoarchaeota Recently added: Oct 12: METMI - Methanococcus maripaludis Jun 30: METP4 - Methanoplanus petrolearius (strain DSM 11571 / OCM 486 / SEBR 4847) Jun 15: VULDI - Vulcanisaeta distributa (strain DSM 14429 / JCM 11212 / NBRC 100878 / IC-017) |
Tree of Bacteria
Tree info: All Bacterial genomes, Wed Jun 27 01:46:01 2007, 340 species, 114863 orthologs, 943 used here, Arithmetic, BestDimlessDimlessQual: best: 4.3995, ave: 4.997 +- 0.011, var: 0.03114, Z=-3.386
Downloads: Unrooted tree (pdf), phylogram (pdf), Newick tree file, PhyloXML tree file or a Darwin script to plot your own tree.
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Color code: Proteobacteria Firmicutes Actinobacteria Cyanobacteria Spirochaetes Bacteroidetes Chlamydiae Chlorobi Deinococcus-Thermus Acidobacteria Chloroflexi Aquificae Fusobacteria Planctomycetes Thermotogales Eukaryota Recently added: Jun 18: YERPN - Yersinia pestis (biovar Antiqua strain Nepal516) Jun 17: VEREI - Verminephrobacter eiseniae (strain EF01-2) Jun 03: DESDG - Desulfovibrio desulfuricans (strain G20) |
Tree of Gammaproteobacteria
Tree info: All Gammaproteobacteria (max Length) (only 1 isoform used) , Sun Dec 19 08:41:07 2010, 224 species, 55894 orthologs, 52 top groups, 277 used here, AveVarWeighted, BestSubsetDimlessQual: best: 0.13535, ave: 0.15494 +- 0.00078, var: 0.0001566, Z=-1.566
Downloads: Unrooted tree (pdf), phylogram (pdf), Newick tree file, PhyloXML tree file or a Darwin script to plot your own tree.
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Color code: Enterobacteriales Alteromonadales Pseudomonas Pasteurellales Xanthomonadales Vibrionales Francisellaceae Moraxellaceae Legionellales Chromatiales Oceanospirillales Acidithiobacillales Aeromonadales sulfur-oxidizing symbionts Piscirickettsiaceae Azotobacter Cellvibrio Baumannia Cardiobacteriales Methylococcales Recently added: Dec 11: LEGLN - Legionella longbeachae serogroup 1 (strain NSW150) Oct 13: ECOD1 - Escherichia coli (strain ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1) Oct 11: CITRI - Citrobacter rodentium (strain ICC168) |
Tree of other Proteobacteria
Tree info: Other Proteobacteria (max Length) (only 1 isoform used) , Tue Mar 8 06:10:21 2011, 236 species, 89463 orthologs, 156 top groups, 451 used here, AveVarWeighted, BestSubsetDimlessQual: best: 0.41814, ave: 0.5786 +- 0.0025, var: 0.001664, Z=-3.934
Downloads: Unrooted tree (pdf), phylogram (pdf), Newick tree file, PhyloXML tree file or a Darwin script to plot your own tree.
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Color code: Rhizobiales Burkholderiales Deltaproteobacteria Epsilonproteobacteria Rickettsia Rhodobacterales Neisseriales Anaplasmataceae Rhodospirillales Sphingomonadales Wolbachieae Rhodocyclales Caulobacterales Methylophilales Nitrosomonadales Orientia SAR11 cluster Hydrogenophilales SAR116 cluster Magnetococcus Recently added: Dec 06: NEIML - Neisseria meningitidis (strain alpha14) Oct 09: PUNMI - Puniceispirillum marinum (strain IMCC1322) Oct 09: METML - Methylotenera mobilis (strain JLW8 / ATCC BAA-1282 / DSM 17540) |
Tree of Firmicutes
Tree info: All Firmicutes (max Length) (only 1 isoform used) , Wed Oct 27 09:21:52 2010, 177 species, 45611 orthologs, 59 top groups, 228 used here, Weighted, BestSubsetDimlessQual: best: 0.26287, ave: 0.3001 +- 0.0010, var: 0.0002853, Z=-2.203
Downloads: Unrooted tree (pdf), phylogram (pdf), Newick tree file, PhyloXML tree file or a Darwin script to plot your own tree.
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Color code: Streptococcus Clostridiales Bacillaceae Staphylococcaceae Lactobacillus Listeriaceae Thermoanaerobacterales Lactococcus Bacillales Family XII. Incertae Sedis Paenibacillaceae Leuconostoc Pediococcus Halanaerobiales Natranaerobiales Alicyclobacillaceae Macrococcus Enterococcaceae Oenococcus Recently added: Oct 09: LACRL - Lactobacillus rhamnosus (strain Lc 705) Aug 16: STRG3 - Streptococcus gallolyticus (strain UCN34) Aug 12: STRS4 - Streptococcus suis (strain BM407) |
Tree of Cyanobacteria
Tree info: All Cyanobacteria (max Length) (only 1 isoform used) , Fri Apr 8 21:02:57 2011, 35 species, 13907 orthologs, 1 top groups, 214 used here, Weighted, BestSubsetDimlessQual: best: 2.0568, ave: 2.2029 +- 0.0086, var: 0.01915, Z=-1.056
Downloads: Unrooted tree (pdf), phylogram (pdf), Newick tree file, PhyloXML tree file or a Darwin script to plot your own tree.
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Color code: Chroococcales Prochlorales Nostocales Acaryochloris Oscillatoriales Recently added: Sep 10: CYAP7 - Cyanothece sp. (strain PCC 7424) Dec 03: CYAP0 - Cyanothece sp. (strain PCC 8802) Jun 14: CYAP4 - Cyanothece sp. (strain PCC 7425 / ATCC 29141) |
Tree of Actinobacteria
Tree info: All Actinobacteria (max Length) (only 1 isoform used) , Thu Dec 16 03:44:52 2010, 85 species, 42935 orthologs, 20 top groups, 214 used here, Weighted, BestSubsetDimlessQual: best: 0.66372, ave: 0.7152 +- 0.0021, var: 0.001103, Z=-1.549
Downloads: Unrooted tree (pdf), phylogram (pdf), Newick tree file, PhyloXML tree file or a Darwin script to plot your own tree.
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Color code: Actinomycetales Bifidobacterium Coriobacteridae Gardnerella Acidimicrobidae Rubrobacteridae Recently added: Dec 10: CORPF - Corynebacterium pseudotuberculosis (strain FRC41) Dec 10: BIFAV - Bifidobacterium animalis subsp. lactis (strain V9) Nov 28: MYCBT - Mycobacterium bovis (strain BCG / Tokyo 172 / ATCC 35737 / TMC 1019) |
Tree of other Bacteria
Tree info: Other Bacteria (max Length) (only 1 isoform used) (VPs consistent per genome-pair) , Mon Apr 2 18:26:11 2012, 174 species, 49530 orthologs, 124 top groups, 245 used here, AveVarWeighted, BestSubsetDimlessQual: best: 0.99973, ave: 1.644 +- 0.039, var: 0.4001, Z=-1.018
Downloads: Unrooted tree (pdf), phylogram (pdf), Newick tree file, PhyloXML tree file or a Darwin script to plot your own tree.
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Color code: Bacteria Recently added: Mar 25: CROAH - Croceibacter atlanticus (strain ATCC BAA-628 / HTCC2559 / KCTC 12090) Mar 24: TREPC - Treponema pallidum subsp. pallidum (strain Chicago) Mar 20: MURRD - Muricauda ruestringensis (strain DSM 13258 / LMG 19739 / B1) |
Tree of Eukaryota
Tree info: All Eukaryotal genomes, Thu Dec 22 16:38:15 2011, 124 species, 258439 orthologs, 77 top groups, 1289 used here, Weighted, BestSubsetDimlessQual: best: 0.032335, ave: 0.05876 +- 0.00024, var: 1.557e-05, Z=-6.697
Downloads: Unrooted tree (pdf), phylogram (pdf), Newick tree file, PhyloXML tree file or a Darwin script to plot your own tree.
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Color code: Chordata Dikarya Protostomia Viridiplantae Pseudocoelomata Euglenozoa Alveolata Microsporidia Echinodermata Acoelomata Cnidaria Placozoa Amoebozoa Choanoflagellida Cryptophyta Fornicata Haptophyceae Recently added: Nov 06: NOMLE - Nomascus leucogenys (Northern white-cheeked gibbon) Oct 15: SARHA - Sarcophilus harrisii (Tasmanian devil) Oct 07: STRPU - Strongylocentrotus purpuratus (Purple sea urchin) |
Tree of Metazoa
Tree info: All Metazoa (max Length) (only 1 isoform used) (VPs consistent per genome-pair) , Sat Jan 7 16:03:00 2012, 79 species, 163698 orthologs, 26 top groups, 850 used here, Arithmetic, BestSubsetDimlessQual: best: 0.032241, ave: 0.04851 +- 0.00015, var: 5.783e-06, Z=-6.767
Downloads: Unrooted tree (pdf), phylogram (pdf), Newick tree file, PhyloXML tree file or a Darwin script to plot your own tree.
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Color code: Theria Protostomia Pseudocoelomata Actinopterygii Sauropsida Tunicata Prototheria Amphibia Cephalochordata Echinodermata Acoelomata Cnidaria Placozoa Recently added: Nov 06: NOMLE - Nomascus leucogenys (Northern white-cheeked gibbon) Oct 15: SARHA - Sarcophilus harrisii (Tasmanian devil) Oct 07: STRPU - Strongylocentrotus purpuratus (Purple sea urchin) |
Tree of Mammalia
Tree info: All Mammalia (max Length) (only 1 isoform used) (VPs consistent per genome-pair) , Fri Dec 23 22:20:39 2011, 39 species, 61714 orthologs, 4 top groups, 479 used here, AveVarWeighted, BestSubsetDimlessQual: best: 0.27374, ave: 0.4133 +- 0.0021, var: 0.001156, Z=-4.102
Downloads: Unrooted tree (pdf), phylogram (pdf), Newick tree file, PhyloXML tree file or a Darwin script to plot your own tree.
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Color code: Laurasiatheria Haplorrhini Glires Afrotheria Metatheria Strepsirrhini Xenarthra Scandentia Prototheria Recently added: Nov 06: Northern white-cheeked gibbon - Nomascus leucogenys Oct 15: Tasmanian devil - Sarcophilus harrisii Dec 27: Giant panda - Ailuropoda melanoleuca |
Tree of other Eukaryota
Tree info: Eukaryota excluding Metazoa (max Length) (only 1 isoform used) (VPs consistent per genome-pair) , Thu Jan 12 17:12:11 2012, 45 species, 92647 orthologs, 24 top groups, 489 used here, Arithmetic, BestSubsetDimlessQual: best: 0.44355, ave: 0.8184 +- 0.0036, var: 0.003351, Z=-6.475
Downloads: Unrooted tree (pdf), phylogram (pdf), Newick tree file, PhyloXML tree file or a Darwin script to plot your own tree.
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Color code: Fungi Viridiplantae Euglenozoa Alveolata Amoebozoa Choanoflagellida Fornicata Haptophyceae Metazoa Recently added: Aug 15: CHLRE - Chlamydomonas reinhardtii May 27: MAIZE - Zea mays (Maize) Apr 14: PUCGT - Puccinia graminis f. sp. tritici (Black rust) |
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