wrightaprilm / charactersimulations

Files related to a phylogenetics project.

CharacterSimulations

Files related to a phylogenetics project exploring missing data and the Mk model Generally, you will want to simulate characters with Hetero_script.R, simulate missing data using new_filter.py, clean up missing data characters with cleaning.sh and assemble the data sets using assemble.sh.

After computing the phylogenies, WRFmorph and WRFparsimony can be used to calculate Robinson-Foulds scores on Bayesian and parsimony trees, respectively. Plot.py is meant to be used interactively in iPython to create graphics.