Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses

Genome Biology

Volumn 12, Issue 2, 2011, Pages

  Vilella, Albert J ^a   Birney, Ewan ^a   Flicek, Paul ^a   Herrero, Javier ^a  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ENSEMBLCOMPARA DATABASE; EUKARYOTE; GENE DUPLICATION; GENE LOSS; GENE SEQUENCE; GENETIC DATABASE; GENETIC MODEL; GENOME; GENOME ANALYSIS; HUMAN; HUMAN GENOME; LETTER; MAMMAL; NONHUMAN; ORTHOLOGY; PHYLOGENETIC TREE ROOT; PHYLOGENY; PLACENTAL MAMMALS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; ANIMAL; COMPARATIVE GENOMIC HYBRIDIZATION; MOLECULAR EVOLUTION; NOTE;

MAMMALIA;

ANIMALS; COMPARATIVE GENOMIC HYBRIDIZATION; EVOLUTION, MOLECULAR; HUMANS; PHYLOGENY;

EID: 79951794116     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2011-12-2-401     Document Type: Letter

References (15)

1. Mammalian Genome Project. , http://www.broadinstitute.org/scientific-community/science/projects/mammals-models/mammalian-genome-project
2. Milinkovitch M, Helaers R, Depiereux E, Tzika A, Gabaldon T. 2X genomes - depth does matter. Genome Biol 2010, 11:R16. 10.1186/gb-2010-11-2-r16, 2872876, 20144222.
3. Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldon T. The human phylome. Genome Biol 2007, 8:R109. 10.1186/gb-2007-8-8-109, 2394744, 17567924.
4. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003, 52:696-704. 10.1080/10635150390235520, 14530136.
5. Zmasek CM, Eddy SR. A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 2001, 17:821-828. 10.1093/bioinformatics/17.9.821, 11590098.
6. Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. EnsemblCompara Gene-Trees: complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 2009, 19:327-335. 10.1101/gr.073585.107, 2652215, 19029536.
7. Ensembl Archives. , http://www.ensembl.org/info/website/archives/index.html
8. TreeSoft: TreeBeST. , http://treesoft.sourceforge.net/treebest.shtml
9. Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Gräf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kähäri A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, et al. Ensembl 2008. Nucleic Acids Res 2008, 36:D707-D714. 10.1093/nar/gkm988, 2238821, 18000006.
10. Dufayard J, Duret L, Penel S, Gouy M, Rechenmann F, Perrière G. Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics 2005, 21:2596-2603. 10.1093/bioinformatics/bti325, 15713731.
11. Wheeler WC. Extinction, sampling, and molecular phylogenetics. Extinction and Phylogeny 1992, 205-215. New York: Columbia University Press, Novacek MD, Wheeler QD.
12. Gatesy J, Milinkovitch M, Waddell V, Stanhope M. Stability of cladistic relationships between Cetacea and higher-level artiodactyl taxa. Syst Biol 1999, 48:6-20. 10.1080/106351599260409, 12078645.
13. Zwickl DJ, Hillis DM. Increased taxon sampling greatly reduces phylogenetic error. Syst Biol 2002, 51:588-598. 10.1080/10635150290102339, 12228001.
14. Tzika A, Helaers R, Van de Peer Y, Milinkovitch MC. MANTiS: a phylogenetic framework for multi-species genome comparisons. Bioinformatics 2008, 24:151-157. 10.1093/bioinformatics/btm567, 18025004.
15. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GR, Ruffier M, Schuster M, et al. Ensembl 2011. Nucleic Acids Res 2011, 39:D800-D806. 10.1093/nar/gkq1064, 3013672, 21045057.