GeLL: a generalized likelihood library for phylogenetic models
2015 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 31, no 14, 2391-2393 p.Article in journal (Refereed) Published
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.
Bioinformatics (Computational Biology) Biochemistry and Molecular Biology
IdentifiersURN: 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].2015-08-212015-08-212015-08-21Bibliographically approved