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 |
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Format: | Artikel |
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. |
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ISSN: | 1471-2105 1471-2105 |
DOI: | 10.1186/1471-2105-14-209 |