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GeLL: a generalized likelihood library for phylogenetic models
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
2015 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 31, no 14, 2391-2393 p.Article in journal (Refereed) Published
Abstract [en]

Phylogenetic models are an important tool in molecular evolution allowing us to study the pattern and rate of sequence change. The recent influx of new sequence data in the biosciences means that to address evolutionary questions, we need a means for rapid and easy model development and implementation. Here we present GeLL, a Java library that lets users use text to quickly and efficiently define novel forms of discrete data and create new substitution models that describe how those data change on a phylogeny. GeLL allows users to define general substitution models and data structures in a way that is not possible in other existing libraries, including mixture models and non-reversible models. Classes are provided for calculating likelihoods, optimizing model parameters and branch lengths, ancestral reconstruction and sequence simulation.

Place, publisher, year, edition, pages
2015. Vol. 31, no 14, 2391-2393 p.
National Category
Bioinformatics (Computational Biology) Biochemistry and Molecular Biology
URN: urn:nbn:se:uu:diva-260626DOI: 10.1093/bioinformatics/btv126ISI: 000358173500025PubMedID: 25725494OAI: oai:DiVA.org:uu-260626DiVA: diva2:847885

This work was supported by the Biotechnology and Biological Sciences Research Council, UK, and National Science Foundation [DEB-0732920 to Mark Holder].

Available from: 2015-08-21 Created: 2015-08-21 Last updated: 2015-08-21Bibliographically approved

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