This repository describes all the steps necessary to do genome-wide Positive selection analysis of the African wild dog (AWD), extract 25-kb alignments from multiple canid genomes for phylogenomic analysis and 1kb alignments for the demographic model.

1. Get variants from raw reads

This step will get BAM files for different canids

All scripts necesary for this step can be found within Get_VCF_from_Reads/

bash from_fastaq_to_VCF.sh

2. Identify selective sweeps

This step will identify windows will low diversity and high divergence among AWD genomes

All scripts necessary for this step can be found within HKA-like_Test/

bash HKA-like.sh

3. Branch-site test with PAML

This step will identify genes with a significant amount of dn/ds changes along the branch of the AWD and the dhole.

All scripts necessary for this step can be found within PAML_Positive_Selection/

bash Positive_selection.sh

4. Get 25kb-alignments

This step will get alignments and best partitions that are necessary for RAXML, ASTRAL and divergence times analysis.

All scripts necessary for this step can be found within 25KB_windows/

bash Get_25kb.sh

5. Get 1kb-alignments

This step will get alignments that are necessary for the demographic model with G-phocs

All scripts necessary for this step can be found within 1kb_alignments_Gphocs/

bash Get_1kb_neutral_loci.sh