Selective Pressure Analysis - Pinnipedia

Vespasian_raw_outputs:

The file "Vespasian_results.0.8-combined" is the outputted file from the Vespasian analysis after it was parsed with a filter script. This contains all the raw outputs from he selective pressure analysis with BEB scores filtered for >0.8. The unique selected sites are the scores for all the sites uniquely selected to a lineage. And then individually broken down into each lineage. 

Gene_analysis:

This directory contains all the analyses I did to attempt to uncover orthologous groups related to different different associated lactation traits. This is quite a messy directory so let me know if there is anything specific you would like to know here.

I have then included some analysis directories I had, looking at each lineage individually. Such as how I performed the enrichment analysis and their related scripts. Again a slightly messy directory so happy to answer any questions on this.

REGs:

This is the analysis for the rapidly evolving site analysis I did for the Caspian and Hooded seal. 

Alignments:

This is a dump of all the alignments I used for the analysis. All_alignments is my raw MSAs before I did any additional filtering for the selection analysis such as pruning for single orthologs. Selected MSAs are the pruned orthologs for all the MSAs I put into Vespasian for each lineage. All_vespasian_MSAs are all the 7000+ MSAs I used in the section analysis.