Bayescode is an ongoing project with several ramifications.
If you want to use the Mutation-Selection framework for detecting site-specific adaptive evolution, please use the following fork of BayesCode: https://github.com/ThibaultLatrille/bayescode.
- Nicolas Rodrigue, Thibault Latrille, Nicolas Lartillot, A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes, Molecular Biology and Evolution, Volume 38, Issue 3, March 2021, Pages 1199–1208, https://doi.org/10.1093/molbev/msaa265
If you want to use the Mutation-Selection framework for inferring long-term effective population size, please use the following fork of BayesCode: https://github.com/ThibaultLatrille/bayescode.
Moreover, the repository at https://github.com/ThibaultLatrille/MutationSelectionDrift is meant to provide the necessary scripts and data to reproduce the figures shown in the manuscript and gives the tools to produce your own experiment on your dataset, given you have at least an DNA alignment file and an associated rooted tree topology (branch lengths are not required).
- Thibault Latrille, Vincent Lanore, Nicolas Lartillot, Inferring Long-Term Effective Population Size with Mutation–Selection Models, Molecular Biology and Evolution, Volume 38, Issue 10, October 2021, Pages 4573–4587, https://doi.org/10.1093/molbev/msab160
$ git clone https://github.com/bayesiancook/bayescode.git
Requirements: mpic++
$ cd ./bayescode/sources
$ make
You can install meson with brew install meson (Mac) or apt install meson (Linux).
$ cd ./bayescode sources
$ meson build -Dprefix=$HOME/Applications/bayescode
$ ninja -C build install
The binaries will end up as e.g. /bin/multigeneaamutselddp.
$ cd ../data
$ mpirun -n 4 multigeneaamutselddp
Nicolas Lartillot (https://github.com/bayesiancook)