This repo contains two programs for studying evolutionary gene flux across a phylogeny:
- GeneFluxAnalysis.py : Wrapper program to automate gene flux analysis using PAUP and post-process results.
- CorStrictor.py : Program to determine the size of the number of single-copy-core genes at each inner-node of the phylogeny.
These wrappers/programs were developed by Rauf Salamzade and Abigail Manson in the Bacterial Genomics Group at the Broad Institute.
Check out the wiki for more information on running the two programs!
If you use GeneFluxAnalysis.py, which uses PAUP (https://paup.phylosolutions.com/) for parsimony based ancestral state reconstruction, please cite:
Swofford, D. L. 2003. PAUP*. Phylogenetic Analysis Using Parsimony (and Other Methods). Version X. Sinauer Associates, Sunderland, Massachusetts. Note: Because there are a number of beta and test versions of the program _you should mention the specific version of PAUP somewhere in the methods._
If you use the interactive tree of life (https://itol.embl.de/) for visualization, please cite:
Letunic I and Bork P (2019) Nucleic Acids Res doi: 10.1093/nar/gkz239 Interactive Tree Of Life (iTOL) v4: recent updates and new developments