Summer/Fall 2015 scripts for running, comparing, and visualizing trees and gene evolution in treespace.
The goal of this repository is intended to display and allow replication of the results in a forthcoming paper on treespace, tree visualizations, and genetic evolutionary model comparisons by Aurora Koch-Pongsema and Assistant Professor Megan Owen at CUNY-Lehman College. For information on the analysis and Sturm_Mean .jar files used to calculate geodesic distance and coordinates, and general information on treespace, please see the publications and contact information at Professor Owen's site.
- *** Note - cleanup and refactoring still in progress ***
- The "Model" + Obj classes were developed to allow batch processing of gene sequences by their respective modelling programs and provides flags for either the K-80 or the GTR-Gamma/GTR-I-Gamma models to be used.
- jarutils provides routines to work with the different jars and their functions.
- Various plotting functions combine Python with R to generate visualizations of treespace under different conditions.
- BayestoDenali works with output from Mr. Bayes to prepare it for use in Denali.
- SequenceGenerator
Python 2.7
R 3.2.0 (or higher)
Genetic evolutionary models
Partial dependencies (only certain scripts)
- Please contact either Aurora Koch-Pongsema at aurora.koch at lc dot cuny dot edu or Professor Megan Owen at megan.owen at lehman dot cuny dot edu for additional information.