jhpanda / drosophilaproteinevolution

Intermolecular interactions drive protein adaptive and co-adaptive evolution at both species and population levels

Scripts and files in this repo:

1. AlternativeGenomes
   scripts to generate alternative genomes or coding sequences based on SNP information, scripts take genome and VCF files as input
2. PPI-sites
   scripts and data to simulate evolutionary rates of protein sites involved in PPI
3. LIG-sites
   scripts and data to simulate evolutionary rates of protein sites involved in LIG binding
4. pyMKT
   scripts to do classic MKT test based on alternative CDS as input
5. MKT
   pyMKT in C version
6. Supplementary files for the paper
7. asymMKfit.py
   script to do asymptotic MK test
8. 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