Overview
This repository contains data and scripts for reproducing the results accompanying the manuscript
Fitness inference from complex evolutionary histories with genetic linkage
Muhammad S. Sohail1,*, Raymond H. Y. Louie1-4,*, Matthew R. McKay1,5,# and John P. Barton6,#
1 Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology
2 Institute for Advanced Study, Hong Kong University of Science and Technology
3 Kirby Institute, University of New South Wales
4 School of Medical Sciences, University of New South Wales
5 Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology
6 Department of Physics and Astronomy, University of California, Riverside
* Equal contributions
# correspondence to m.mckay@ust.hk and jpbarton@pitt.edu
Contents
Scripts for generating and analyzing the simulation data can be found in the simulation-analysis.ipynb notebook, and references therein. Scripts for processing and analyzing the HIV-1 data are contained in the HIV-analysis.ipynb notebook. Finally, scripts for analysis and figures contained in the manuscript are located in the figures.ipynb notebook.
Due to the large size and number of some files generated by simulations and by the interim analysis of HIV-1 data, some data has been stored in a compressed format using Zenodo. To access the full set of data, navigate to the Zenodo record. Then download and extract the contents of the archives src-MPL-HIV.tar.gz, src-wfsim-data.tar.gz, and src-Matlab-data.tar.gz into the folders src/MPL/HIV, src/wfsim/data, and src/Matlab, respectively.
MPL
This repository includes code for inferring selection coefficients from temporal genetic data using the marginal path likelihood (MPL) method. Code implementing MPL in C++ is located in the src/MPL directory.
Software dependencies
MPL makes use of C++11 and the GNU Scientific Library. The code has been tested using GSL version 2.6. Compiling MPL should require a few seconds on a typical desktop computer.
Demonstration
The shell script src/MPL/run-test.sh will compile and run MPL on an example set of simulation data (see Figure 1 in the manuscript). Estimated selection coefficients are stored in src/MPL/test/example_0_T400_ns1000_dt1_MPL.dat. This file should match the file of the same name in the src/MPL/out directory. Running this demonstration should require a few seconds on a typical desktop computer.
License
This repository is dual licensed as GPL-3.0 (source code) and CC0 1.0 (figures, documentation, and our presentation of the data).