GenPhyloData: realistic simulation of gene family evolution

PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process and--perhaps more interestingly--also supports generation of gene family trees guided by a known...

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Veröffentlicht in:BMC bioinformatics 2013-06, Vol.14 (1), p.209-209, Article 209
Hauptverfasser: Sjöstrand, Joel, Arvestad, Lars, Lagergren, Jens, Sennblad, Bengt
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Sprache:eng
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Zusammenfassung:PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process and--perhaps more interestingly--also supports generation of gene family trees guided by a known (synthetic or biological) species tree while accounting for events such as gene duplication, gene loss, and lateral gene transfer (LGT). The suite also supports a wide range of branch rate models enabling relaxation of the molecular clock. Simulated data created with PrIME-GenPhyloData can be used for benchmarking phylogenetic approaches, or for characterizing models or model parameters with respect to biological data. The concept of tree-in-tree evolution can also be used to model, for instance, biogeography or host-parasite co-evolution.
ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-14-209