# ChromoSSE: Cladogenetic and Anagenetic Models of Chromosome Number Evolution This repository contains the scripts used to run the ChromoSSE phylogenetic models of chromosome number evolution. These models allow one to infer the mode of chromosome number evolution; is chromosome evolution occurring primarily within lineages, primarily at lineage splitting, or in clade-specific combinations of both? Furthermore, they estimate the location and timing of possible chromosome speciation events over the phylogeny as well as ancestral chromosome numbers. ChromoSSE was implemented in a Bayesian statistical framework, specifically in the software [RevBayes](http://revbayes.com), to accommodate uncertainty in parameter estimates while leveraging the full power of likelihood based methods. Provided here are the Rev scripts needed to run ChromoSSE in [RevBayes](http://revbayes.com). Please modify these scripts to use your own data, and feel free to contact me with any questions. ### Updates: Please see https://github.com/wf8/chromosse for the latest version of these scripts. ### Tutorial: I've written a tutorial on how to use RevBayes for a wide range of chromosome evolution analyses using ChromEvol, BiChroM, ChromoSSE and other related models: * [Tutorial (pdf)](https://github.com/revbayes/revbayes_tutorial/raw/master/tutorial_TeX/RB_Chromosome_Evolution_Tutorial/RB_Chromosome_Evolution_Tutorial.pdf) * [Example scripts](http://rawgit.com/revbayes/revbayes_tutorial/master/RB_Chromosome_Evolution_Tutorial/scripts.zip) * [Example data](http://rawgit.com/revbayes/revbayes_tutorial/master/RB_Chromosome_Evolution_Tutorial/data.zip) ### Citation: Freyman, W.A. and S. Höhna. Submitted to *Systematic Biology*. Cladogenetic and Anagenetic Models of Chromosome Number Evolution: a Bayesian Model Averaging Approach. [preprint](http://biorxiv.org/content/early/2016/11/16/086629) ### To run an example ChromoSSE analysis: ``` cd examples/aristolochia/ rb aristolochia_analysis.Rev ``` ### To plot the output of a ChromoSSE analysis: Use the [RevGadgets](https://github.com/revbayes/RevGadgets) R package and [this example R script](plot_results.R) to generate figures like this: ![ChromoSSE plot](examples/aristolochia/data/aristolochia_ancestral_states.jpg) ### Contact: Will Freyman, UC Berkeley freyman@berkeley.edu [http://willfreyman.org](http://willfreyman.org)