ReadMapping_VariantCalling.sh :
Bash script to download all astyanax mexicanus reads, map them to the surface reference genome, perform the variant calling and the annotation of variants with Ensembl VEP.
GeneAnnotation_Comparison_Ensembl.sh:
Bash script to compare Astyanax mexicanus gene annotations with 10 other species. Resulting files can be found on this github repo (Transcript_protlen.tsv, Conserved_domains_Amex_trimal.csv). Some scripts called in GeneAnnotation_Comparison_Ensembl.sh can also be found here (Python_Conversion_trimal_Amex.py, Trimal_To_Gblock.py, rename_fasta.pl)
Astyanax_Pseudogene_analysis.R:
This Rscript need results files generated with ReadMapping_VariantCalling.sh and GeneAnnotation_Comparison_Ensembl.sh. This annotated Rscript allows to perform all the analysis presented in the manuscript.