Code and data for "Limited Utility of Residue Masking for Positive-Selection Inference," by SJS, ETD, COW.
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PhyloGuidance self.srcdir Dec 16, 2014
data readme info for data moved to own file May 29, 2014
scripts added info on countGaps.py May 29, 2014
README.md added citation Jun 4, 2014

README.md

alignment_filtering

This repository contains materials used for the manuscript, Limited utility of residue masking for positive-selection inference Stephanie J. Spielman; Eric T. Dawson; Claus O. Wilke Molecular Biology and Evolution 2014; doi: 10.1093/molbev/msu183

Please direct all questions to Stephanie, at stephanie.spielman@gmail.com (or stephanie.spielman@utexas.edu).

Description of directories and contents as follows.

PhyloGuidance/ Contains all code and a README file to run our re-implemented Guidance, PhyloGuidance. See the README within that directory for details. Note that the name "PhyloGuidance" doesn't carry over into the manuscript, but it is probably a nicer name for this directory than "Guidance_Reimplementation."

data/ Contains final parsed data files and statistics. See README within for details.

scripts/ Contains code for analyses conducted in manuscript, including sequence simulation, selection inference with FUBAR and PAML M8, and parsing of the raw data files. All alignments were conducted within PhyloGuidance. The README in the scripts/ directory contains more details.