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GenPhyloData: realistic simulation of gene family evolution

Joel Sjöstrand14, Lars Arvestad145, Jens Lagergren34 and Bengt Sennblad24*

Author Affiliations

1 Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden

2 Department of Medicine, Karolinska Institutet, Atherosclerosis Research Unit, Stockholm, Sweden

3 School of Computer Science and Communications, KTH Royal Institute of Technology, Stockholm, Sweden

4 Science for Life Laboratory, Stockholm, Sweden

5 Swedish e-Science Research Centre, Stockholm, Sweden

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BMC Bioinformatics 2013, 14:209  doi:10.1186/1471-2105-14-209

Published: 27 June 2013

Abstract

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.

Keywords:
Phylogenetics; Synthetic data; Gene family; Gene duplication; Gene loss; LGT; Molecular clock; Biogeography; Host-parasite co-evolution