About ProcessCount

This repository contains the python script total_posteriors_Count.py to calculate the total gene presences, multi, gains, losses, expansions, contractions ocurring per each branch/node in a phylogenetic tree.

Input file is the table resulting from Posteriors analysis made with the software Count: http://www.iro.umontreal.ca/~csuros/gene_content/count.html

Output is written to Total_Posteriors_Count.txt.

Before running the script

Install the following python packages: argparse, pandas, re, math, sys

Running the script

python total_posteriors_Count.py -h
python total_posteriors_Count.py --posteriors <input/posteriors_table.csv>

Citation

Paula Ramos-Silva, Mónica Serrano, Adriano O Henriques, From Root to Tips: Sporulation Evolution and Specialization in Bacillus subtilis and the Intestinal Pathogen Clostridioides difficile, Molecular Biology and Evolution, Volume 36, Issue 12, December 2019, Pages 2714–2736, https://doi.org/10.1093/molbev/msz175