Repository for " Extensively-parameterized mutation–selection models reliably capture site-specific selective constraint" by SJS and COW.
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data
final_submission
inference
postprocessing
results
simulation
.gitignore
README.md
universal_functions.py

README.md

Repository for Extensively parameterized mutation–selection models reliably capture site-specific selective constraint, by SJS* and COW.

Please cite the following article, as needed: http://mbe.oxfordjournals.org/content/early/2016/08/10/molbev.msw171.abstract

Contents of repository:

  • data/ contains all simulated alignments, and the 512-taxon balanced trees (with branch lengths of either 0.5 or 0.01) used during simulation. Alignments are named with this format: <dataset_name>_bl<0.5/0.01>.phy, where bl indicates the branch lengths of the tree used for simulation.

  • simulation/ contains all code used for simulating sequences, as well as simulating parameters for use in sequence simulation.

  • inference/ contains all code used for mutation-selection model inference. All scripts named *.sh and *.qsub are used for submitting jobs to UT's Phylocluster, and all *.py scripts conduct and process inferences.

  • results/ contains all inference results.

    • swmutsel/ contains all inference results with swMutSel for a variety of penalizations, indicated in file name. The script ./results/extract_sw_fitness.py extracts fitness values from the MLE inferences from swMutSel into separate text files for later use
    • phylobayes/ contains all inference results with pbMutSel
  • postprocessing/ contains all code used to process, analyze, and plot data (mostly R scripts). All generated plots are also in this directory. All scripts should be executed from this directory! Note: R code requires the packages (and their dependencies) cowplot, ggrepel, dplyr, tidyr, readr, grid, lme4, multcomp, and lmerTest.

  • universal_functions.py is a python module containing various functions used throughout the repository.

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