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

Bioinformatics. 2014 Aug 1;30(15):2216-8. doi: 10.1093/bioinformatics/btu181. Epub 2014 Apr 10.


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 All source code is also available on github geiger v2.0 depends on the ape package.


Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Bayes Theorem
  • Biological Evolution*
  • Computational Biology / methods*
  • Likelihood Functions
  • Models, Biological*
  • Phylogeny*
  • Programming Languages*