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

Matthew W. Pennell*, Jonathan M. Eastman, Graham J. Slater, Joseph W. Brown, Josef C. Uyeda, Richard G. Fitzjohn, Michael E. Alfaro, Luke J. Harmon

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

232 Citations (Scopus)

Abstract

Summary: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. Supplementary information:Supplementary data are available at Bioinformatics online

Original languageEnglish
Pages (from-to)2216-2218
Number of pages3
JournalBioinformatics
Volume30
Issue number15
DOIs
Publication statusPublished - 1 Aug 2014

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