Selective Pressure Analysis - Pinnipedia

<p>Vespasian_raw_outputs:</p> <p>The file &quot;Vespasian_results.0.8-combined&quot; 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 &gt;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.&nbsp;</p> <p>&nbsp;</p> <p>Gene_analysis:</p> <p>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.</p> <p>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.</p> <p>REGs:</p> <p>This is the analysis for the rapidly evolving site analysis I did for the Caspian and Hooded seal.&nbsp;</p> <p>Alignments:</p> <p>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&nbsp;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.</p> <p>&nbsp;</p> <p>&nbsp;</p> <p>&nbsp;&nbsp;&nbsp;</p>