/Gesneriaceae-Diversification

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Gesneriaceae Diversification

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Roalson EH, Roberts WR. 2016. Distinct Processes Drive Diversification in Different Clades of Gesneriaceae. Systematic Biology 65(4): 662-684.

Scripts written in R and Python for analyses performed in the study. Written by W.R. Roberts.

  1. BiSSE - state-dependent diversification rate estimates for epiphytism, unifoliate growth, and bird-pollination.

  2. GeoSSE - state-dependent diversification rate estimates for presence in Andes, Africa, Caribbean, Brazil, and Southeast Asia.

  3. ExaML - python wrapper for building large ML phylogenies from a directory of phylip alignment files, useful for bootstrap alignments.

  4. TreePL - python wrapper for dating the bootstrap trees after estimating their branch lengths with ExaML. This takes a directory of directory of trees, reroots the trees (if necessary), and estimates dates using penalized likelihood. Parameters can be adjusted as needed for a particular dataset.