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GenPhyloData: realistic simulation of gene family evolution
Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden .
Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden .
KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, Science for Life Laboratory, SciLifeLab.
Department of Medicine, Karolinska Institutet, Atherosclerosis Research Unit, Stockholm, Sweden .
2013 (English)In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 14, no 1, 209- p.Article in journal (Refereed) Published
Abstract [en]

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.
Keyword [en]
Phylogenetics, Synthetic data, Gene family, Gene duplication, Gene loss, LGT, Molecular clock, Biogeography, Host-parasite co-evolution
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-124972DOI: 10.1186/1471-2105-14-209ISI: 000321381300001Scopus ID: 2-s2.0-84879430245OAI: oai:DiVA.org:kth-124972DiVA: diva2:638934
Funder
Swedish Research Council, 2010-4757 2010-4634Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish e‐Science Research Center
Note

QC 20130805

Available from: 2013-08-05 Created: 2013-08-02 Last updated: 2017-12-06Bibliographically approved

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Sjöstrand, JoelArvestad, LarsLagergren, JensSennblad, Bengt
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