GeLL: a generalized likelihood library for phylogenetic models.
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.


METHODS
http://phylo.bio.ku.edu/GeLL under a GPL v3 license.
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.
Daniel
D
Money
Department of Evolutionary Biology, Uppsala University, Uppsala, 75236, Sweden.
Simon
S
Whelan
D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D012984:Software