GenPhyloData: realistic simulation of gene family evolution
2013 (English)In: BMC Bioinformatics, ISSN 1471-2105, Vol. 14, 209Article in journal (Refereed) Published
Background: 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. Result: 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. Conclusion: The concept of tree-in-tree evolution can also be used to model, for instance, biogeography or host-parasite co-evolution.
Place, publisher, year, edition, pages
2013. Vol. 14, 209
Phylogenetics, Synthetic data, Gene family, Gene duplication, Gene loss, LGT, Molecular clock, Biogeography, Host-parasite co-evolution
Biochemistry and Molecular Biology Microbiology
IdentifiersURN: urn:nbn:se:su:diva-92509DOI: 10.1186/1471-2105-14-209ISI: 000321381300001OAI: oai:DiVA.org:su-92509DiVA: diva2:639770