Repository for "A comparison of one-rate and two-rate inference frameworks for site-specific dN/dS estimation" by SJS*, SW, COW.

Contents of repository:

• count_substitutions/ contains code and results for substitutions counted along simulations using ancestral sequences.

• dnds_inference/ contains all HyPhy code and batchfiles for inferring dN/dS.

• results/ contains all dN/dS inference files made by HyPhy, for both simulations along balanced trees and empirical trees. The directory unequalpi_nucfits/ contains results for the nucleotide fits that HyPhy performs before rate calculation (branch lengths are optimized here). The files here are specifically from SLAC inference. Note that all inference methods, as coded in HyPhy, employ more or less the same procedure for nucleotide fits (slight FUBAR exception, although not terribly different), so this data applies across all methods examined here.

• trees/ contains all trees used for simulation, as well as a simple script to calculate tree statistic for empirical phylogenies. You can grab all simulated alignments fromg this Google Drive folder. If that link is broken, please contact me at stephanie.spielman@gmail.com.

• simulation/ contains all scripts and data files used during sequence simulation, as well as true simulation parameters.

• postprocessing/ contains R code for statistical analyses, processed results (into CSV files), and figures. Note that processed result files are in the subdirectory dataframes/, and all figures are in the subdirectory figures/ (further organized into maintext/ and SI/ for figures in the main text and supplementary info, respectively).

Note that all scripts named *.sh and *.slurm were used for submitting jobs to TACC.

*This repository is maintained by SJS. Please file any questions/comments in Issues, or email stephanie.spielman@gmail.com