geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees

• Published in: Bioinformatics (Oxford, England) Vol. 30; no. 15; pp. 2216 - 2218
• Main Authors: Pennell, Matthew W., Eastman, Jonathan M., Slater, Graham J., Brown, Joseph W., Uyeda, Josef C., FitzJohn, Richard G., Alfaro, Michael E., Harmon, Luke J.
• Format: Journal Article
• Language: English
• Published: England 01.08.2014
• Subjects: Algorithms; Bayes Theorem; Biological Evolution; Computational Biology - methods; Likelihood Functions; Models, Biological; Phylogeny; Programming Languages
• ISSN: 1367-4803; 1367-4811; 1367-4811
• DOI: 10.1093/bioinformatics/btu181

Phylogenetic comparative methods are essential for addressing evolutionary hypotheses with interspecific data. The scale and scope of such data have increased dramatically in the past few years. Many existing approaches are either computationally infeasible or inappropriate for data of this size. To address both of these problems, we present geiger v2.0 , a complete overhaul of the popular R package geiger . We have reimplemented existing methods with more efficient algorithms and have developed several new approaches for accomodating heterogeneous models and data types. Availability and implementation:  This R package is available on the CRAN repository http://cran.r-project.org/web/packages/geiger/ . All source code is also available on github http://github.com/mwpennell/geiger-v2 . geiger v2.0 depends on the ape package. Contact:   mwpennell@gmail.com Supplementary information:   Supplementary data are available at Bioinformatics online