EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.
We have developed a comprehensive gene orientated phylogenetic resource, EnsemblCompara GeneTrees, based on a computational pipeline to handle clustering, multiple alignment, and tree generation, including the handling of large gene families. We developed two novel non-sequence-based metrics of gene tree correctness and benchmarked a number of tree methods. The TreeBeST method from TreeFam shows the best performance in our hands. We also compared this phylogenetic approach to clustering approaches for ortholog prediction, showing a large increase in coverage using the phylogenetic approach. All data are made available in a number of formats and will be kept up to date with the Ensembl project.
Vilella
Albert J
AJ
EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.
Severin
Jessica
J
Ureta-Vidal
Abel
A
Heng
Li
L
Durbin
Richard
R
Birney
Ewan
E
D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D020440:Gene Duplication; D006801:Humans; D008954:Models, Biological; D005810:Multigene Family; D010802:Phylogeny; D017385:Sequence Homology; D012984:Software; D026801:Synteny; D014714:Vertebrates / Q000145:classification* / Q000235:genetics