Code used for comparative genomic analysis and final data analysis

This repository contains all code used to conduct comparative genomic analyses: a) extraction of 4-fold degenerate sites for estimating neutral rates; b) synteny analysis to identify best orthologs; c) filtering of multiple sequence alignments; and d) phyloP test. Also included is the code used to make figures and conduct final analyses on RNAseq, gene enrichment analysis, and GO/KEGG term enrichment.