Repository for code relating to the analysis of brood parasite genomes to look for convergence.
Steps:
- Whole Genome Alignment using progressiveCactus (details in 01_alignment subdirectory)
- Extract CNEEs from previous work and analyze using phyloAcc (details in 02_CNEEs subdirectory)
- Annotate genomes with CAT (details in 03_CAT subdirectory)
- Some early analysis of protein coding genes
More to come...this is very much a work in progress, code may change without warning.