This is the repository for the collected scripts used in the study "Consequences of asexuality in natural populations: insight from stick insects" (Bast et al. 2018, MBE).
The frozen code at the time of publication can be found here: https://github.com/jensbast/TimemaConsOfAsex/releases/tag/v1.0
- pNpS estimates - scripts for calculation of synonymous and non-synonymous SNPs
- dNdS estimates - script that uses alignments and RaXML branch-lengths calculate dN dS with codeml in the PAML package and outputs a table with all metrics
- augment_OG.ipynb - script (ipython notebook) to mine ortholog variants from the OMA ouput
- polymorphisms_processing.R - R script to process output from pNpS program and calculate pS, pN and pNpS
- commands_orth_algn_raxml - one-liner collection for getting the shared orthologous groups for all ten species, aligning them and running RAxML and preparation to run the dN/dS estimates