asymptoticMK

A tool for computing alpha, the fraction of nucleotide substitutions in a given genomic region that were driven to fixation by positive selection.

Citation: B.C. Haller, P.W. Messer. (2017). asymptoticMK: A web-based tool for the asymptotic McDonald–Kreitman test. G3: Genes, Genomes, Genetics 7(5), 1569–1575.

A web version of this software is available at http://benhaller.com/messerlab/asymptoticMK.html. This source repository is intended for users who wish to run asymptoticMK on their local machine, or wish to modify asymptoticMK for their own use.

  Files

• asymptoticMK_local.R : an R script for running asymptoticMK locally
• asymptoticMK_run.html.R : the web-based version, using FastRWeb
• asymptoticMK.html : the HTML splash page for the web-based version
• LICENSE : the full GNU GPL v.3 license for asymptoticMK
• README.md : this readme file
• sample_polymorphism_levels.txt : a sample Drosophila dataset (use with d=59570, d0=159058)
• simulate_alpha.slim : a SLIM model to generate simulated data for testing asymptoticMK

License

Copyright (c) 2017 Philipp Messer. All rights reserved.

asymptoticMK is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

asymptoticMK is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with asymptoticMK. If not, see http://www.gnu.org/licenses/.

Development & Feedback

If you have feedback or feature requests, or if you are interested in contributing to asymptoticMK, please contact Philipp Messer at messer@cornell.edu. Please note that Philipp is also looking for graduate students and postdocs.