Unusual mammalian usage of TGA stop codons reveals that sequence conservation need not imply purifying selection

Scripts and files for the associated PLoS Biology publication: "Unusual mammalian usage of TGA stop codons reveals that sequence conservation need not imply purifying selection)"

This repository contains source code for running the core analysis described in the paper. Sequences, protein abundance data, recombination rates, etc. should be downloaded from their respective repositories as outlined in our methods. For ease, useful scripts may be found within folders that correspond to the relevant part of the methods section of the paper:

• Inferring stop codon switches from eukaryotic triplets
• Predicting equilibrium TGA content using flux data
• Null simulations to assign significance to observed pTGA deviation between two groups of genes
• Calculating mutational equilibria
• Assessing the predictive abilities of gene expression and recombination rate
• PGLS analysis of TGA enrichment and effective population size (Ne)
• Markov models for simulating null sequences

Note: there is no folder for "Gene expression metrics" nor "Pseudo-autosomal regions, chromosome size, and local recombination rates" as no scripts are necessary for this section of the methods.

Note also: You will find a script called "generic.py". This is a module written and maintained by the Hurst lab that contains generic utility functions that make life a bit easier.

In addition to the scripts, here you will also find various accessions and species lists required for repetition of our analyses. If you wish to completely replicate any of our results, please send me an e-mail and we can sort something out (a.t.ho@bath.ac.uk / xandertho@gmail.com).

Wishing you all the best with your research,

Alexander T. Ho