GenPhyloData: realistic simulation of gene family evolution
2013 (English)In: BMC Bioinformatics, ISSN 1471-2105, Vol. 14, no 1, 209- p.Article 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
BioMed Central, 2013. Vol. 14, no 1, 209- p.
Phylogenetics, Synthetic data, Gene family, Gene duplication, Gene loss, LGT, Molecular clock, Biogeography, Host-parasite co-evolution
Biochemistry and Molecular Biology
IdentifiersURN: urn:nbn:se:kth:diva-124972DOI: 10.1186/1471-2105-14-209ISI: 000321381300001ScopusID: 2-s2.0-84879430245OAI: oai:DiVA.org:kth-124972DiVA: diva2:638934
FunderSwedish Research Council, 2010-4757 2010-4634Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish e‐Science Research Center
QC 201308052013-08-052013-08-022013-12-09Bibliographically approved