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Bioinformatics. 2015 Jul 15;31(14):2391-3. doi: 10.1093/bioinformatics/btv126. Epub 2015 Feb 27.

GeLL: a generalized likelihood library for phylogenetic models.

Author information

1
Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, B2N 5E3 Canada, Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA and.
2
Department of Evolutionary Biology, Uppsala University, Uppsala, 75236, Sweden.

Abstract

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.

AVAILABILITY AND IMPLEMENTATION:

http://phylo.bio.ku.edu/GeLL under a GPL v3 license.

PMID:
25725494
DOI:
10.1093/bioinformatics/btv126
[Indexed for MEDLINE]

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