期刊
BMC BIOINFORMATICS
卷 14, 期 -, 页码 -出版社
BMC
DOI: 10.1186/1471-2105-14-209
关键词
Phylogenetics; Synthetic data; Gene family; Gene duplication; Gene loss; LGT; Molecular clock; Biogeography; Host-parasite co-evolution
类别
资金
- Swedish Research Council [2010-4757, 2010-4634]
- Magnus Bergvall foundation
- Stiftelsen for gamla tjanarinnor
- Karolinska Institutet
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.
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