Introduction

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

Publications

  1. GeLL: a generalized likelihood library for phylogenetic models.
    Cite this
    Money D, Whelan S, 2015-07-01 - Bioinformatics (Oxford, England)

Credits

  1. Daniel Money
    Developer

    Department of Plant and Animal Sciences, Faculty of Agriculture

  2. Simon Whelan
    Investigator

    Department of Evolutionary Biology, Uppsala University, Sweden

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Summary
AccessionBT006506
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionSweden
Submitted BySimon Whelan