Intermolecular interactions drive protein adaptive and co-adaptive evolution at both species and population levels
Scripts and files in this repo:
- AlternativeGenomes
scripts to generate alternative genomes or coding sequences based on SNP information, scripts take genome and VCF files as input - PPI-sites
scripts and data to simulate evolutionary rates of protein sites involved in PPI - LIG-sites
scripts and data to simulate evolutionary rates of protein sites involved in LIG binding - pyMKT
scripts to do classic MKT test based on alternative CDS as input - MKT
pyMKT in C version - Supplementary files for the paper
- asymMKfit.py
script to do asymptotic MK test - groups_gene.dat
genes in each dnds group as in "Supp file S2 Expression Level and Protein Length in each Gene Group.csv"
Reference:
Intermolecular interactions drive protein adaptive and co-adaptive evolution at both species and population levels
Junhui Peng, Nicolas Svetec, Li Zhao
bioRxiv (https://www.biorxiv.org/content/10.1101/2021.02.08.430345v3)
DOI: doi.org/10.1101/2021.02.08.430345