Phylogenetic Tree Construction with TreeFam v4

Seventeen new species have been added since TreeFam v1 (4 (link)). TreeFam v4 contains predicted protein sequences from the fully sequenced genomes of 25 animal species: human, chimpanzee, macaque, mouse, rat, cow, dog, opossum, chicken, frog, two pufferfish (Takifugu and Tetraodon), zebrafish, medaka, stickleback, sea squirts (Ciona intestinalis and C. savignyi), two fruit-flies (Drosophila melanogaster and D. pseudoobscura), two mosquitoes (Aedes aegypti and Anopheles gambiae), the flatworm Schistosoma mansoni, and the nematodes Caenorhabditis elegans, C. briggsae and C. remanei. In addition, four outgroup genomes are included: baker's yeast, fission yeast, rice and thale cress (Arabidopsis).
The C. briggsae and C. remanei proteins were downloaded from WormBase (16 (link)), D. pseudoobscura proteins from FlyBase (17 (link)), fission yeast and flatworm proteins from GeneDB (18 (link)), thale cress proteins from TIGR (19 (link)), rice proteins from the Beijing Genomics Institute (20 (link)) and the remaining sequences from Ensembl (15 (link)). In addition to these species, TreeFam includes UniProt (21 (link)) proteins from animal species whose genomes have not been fully sequenced. For TreeFam v4, all sequences were downloaded in October 2006.

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Ruan J., Li H., Chen Z., Coghlan A., Coin L.J., Guo Y., Hériché J.K., Hu Y., Kristiansen K., Li R., Liu T., Moses A., Qin J., Vang S., Vilella A.J., Ureta-Vidal A., Bolund L., Wang J, & Durbin R. (2007). TreeFam: 2008 Update. Nucleic Acids Research, 36(Database issue), D735-D740.

Publication 2007

Aedes Animal Anopheles gambiae Arabidopsis Baker yeast C proteins Caenorhabditis elegans Chicken Chimpanzee Ciona intestinalis Drosophila melanogaster Fission yeast Flatworm Frog Fruit flies Genomes Human Macaque Medaka Mosquitoes Mouse Nematodes Opossum Protein sequences Proteins Proteins link Pufferfish Rice Schistosoma mansoni Sea squirts Stickleback Takifugu Thale cress Thale cress proteins Zebrafish

Corresponding Organization : BGI Group (China)

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