TreeFam v9: A new website, more species and orthology-on-the-fly

Nucleic Acids Research

Volumn 42, Issue D1, 2014, Pages

  Schreiber, Fabian ^a,b   Patricio, Mateus ^b   Muffato, Matthieu ^b   Pignatelli, Miguel ^b   Bateman, Alex ^b  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ANIMAL GENETICS; ARTICLE; CODON; GENE DUPLICATION; GENE LOSS; GENE MAPPING; GENE SEQUENCE; GENETIC DATABASE; HIDDEN MARKOV MODEL; MULTIGENE FAMILY; NONHUMAN; ONLINE SYSTEM; ORTHOLOGY; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN DOMAIN; SEQUENCE HOMOLOGY; TREEFAM V9 DATABASE; WEB BROWSER; ANIMAL; GENOME; INTERNET; PHYLOGENY; GENE DOSAGE; SEQUENCE ALIGNMENT; TREEFAM V9;

ANIMALS; DATABASES, GENETIC; GENOME; INTERNET; MULTIGENE FAMILY; PHYLOGENY;

ANIMALIA;

EID: 84891766808     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1055     Document Type: Article

References (24)

1. Fitch, W.M. (1970) Distinguishing homologous from analogous proteins. Syst. Zool., 19, 99-113.
2. Li, H., Coghlan, A., Ruan, J., Coin, L. and Heriche, J. (2006) TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res., 34, D572-D580.
3. Ruan, J., Li, H., Chen, Z., Coghlan, A., Coin, L.J.M., Guo, Y., Heriche, J.-K., Hu, Y., Kristiansen, K., Li, R. et al. (2008) TreeFam: 2008 update. Nucleic Acids Res., 36, D735-D740.
4. Mi, H., Muruganujan, A. and Thomas, P.D. (2012) PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res., 41, D377-D386.
5. Vilella, A., Severin, J., Ureta-Vidal, A., Heng, L.L., Durbin, R. and Birney, E. (2009) EnsemblCompara genetrees: complete, duplication-aware phylogenetic trees in vertebrates. Genome Res., 19, 327-335.
6. Datta, R.S., Meacham, C., Samad, B., Neyer, C. and Sjolander, K. (2009) Berkeley PHOG: PhyloFacts orthology group prediction web server. Nucleic Acids Res., 37, W84-W89.
7. Dehal, P.S. and Boore, J.L. (2006) A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database. BMC Bioinformatics, 7, 201.
8. Huerta-Cepas, J., Capella-Gutierrez, S., Pryszcz, L.P., Denisov, I., Kormes, D., Marcet-Houben, M. and Gabaldon, T. (2011) PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Res., 39, D556-D560.
9. Schreiber, F. and Sonnhammer, E.L.L. (2013) Hieranoid: hierarchical orthology inference. J. Mol. Biol., 425, 2072-2081.
10. Altenhoff, A.M., Schneider, A., Gonnet, G.H. and Dessimoz, C. (2011) OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res., 39, D289-D294.
11. Waterhouse, R.M., Tegenfeldt, F., Li, J., Zdobnov, E.M. and Kriventseva, E.V. (2013) OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. Nucleic Acids Res., 41, D358-D365.
12. Chen, F., Mackey, A., Stoeckert, C. Jr and Roos, D. (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res., 34, 363-368.
13. Yook, K., Harris, T.W., Bieri, T., Cabunoc, A., Chan, J., Chen, W.J., Davis, P., de la Cruz, N., Duong, A., Fang, R. et al. (2012) WormBase 2012: more genomes, more data, new website. Nucleic Acids Res., 40, D735-D741.
14. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. and Madden, T.L. (2009) BLAST+: architecture and applications. BMC Bioinformatics, 10, 421.
15. Eddy, S.R. (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform., 23, 205-211.
16. Wallace, I.M., O'Sullivan, O., Higgins, D.G. and Notredame, C. (2006) M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res., 34, 1692-1699.
17. Katoh, K. and Standley, D.M. (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol., 30, 772-780.
18. Li, H. (2006) Constructing the TreeFam database. PhD Thesis. Wellcome Trust Sanger Institute.
19. NCBI Resource Coordinators. (2012) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 41, D8-D20.
20. Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J. et al. (2012) The Pfam protein families database. Nucleic Acids Res., 40, D290-D301.
21. Burge, S.W., Daub, J., Eberhardt, R., Tate, J., Barquist, L., Nawrocki, E.P., Eddy, S.R., Gardner, P.P. and Bateman, A. (2013) Rfam 11.0: 10 years of RNA families. Nucleic Acids Res., 41, D226-D232.
22. Berger, S.A., Krompass, D. and Stamatakis, A. (2011) Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood. Syst. Biol., 60, 291-302.
23. Loytynoja, A., Vilella, A.J. and Goldman, N. (2012) Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics, 28, 1684-1691.
24. Robinson, D.F. and Foulds, L.R. (1981) Comparison of phylogenetic trees. Math. Biosci., 53, 131-147.