BayesCode

The precompiled binaries are available as the bayescode conda package from the channel bioconda:

conda install -c conda-forge -c bioconda bayescode

Wiki and documentation at github.com/ThibaultLatrille/bayescode/wiki

Wiki table of contents

• Installation
• Format your data
• Run BayesCode
• mutselomega - Gene and site-specific rates of evolution (ω, ω₀, ω_A^phy, ω_∗) and selection coefficients (S₀)
• nodemutsel - Changes of effective population size (N_e) and mutation rate (μ) along the phylogeny
• nodeomega - Changes of ω along the phylogeny
• nodetraits - Test of diversifying selection for a quantitative trait
• Citations

References

• The preprint for use of nodetraits to compute ρ is:

T. Latrille, M. Bastian, T. Gaboriau, N. Salamin,
Detecting diversifying selection for a trait from within and between-species genotypes and phenotypes,
bioRxiv,
doi.org/10.1101/2023.10.02.559886

Scripts and data necessary to reproduce figures at github.com/ThibaultLatrille/MicMac.

• The preprint for use of mutselomega to compute S₀ is:

T. Latrille, J. Joseph, D. A. Hartasánchez, N. Salamin,
Mammalian protein-coding genes exhibit widespread beneficial mutations that are not adaptive,
bioRxiv,
doi.org/10.1101/2023.05.03.538864

Scripts and data necessary to reproduce figures at github.com/ThibaultLatrille/SelCoeff.

• If you use mutselomega to compute ω₀ or ω_A^phy = ω - ω₀, please cite:

Thibault Latrille, Nicolas Rodrigue, Nicolas Lartillot,
Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale,
Proceedings of the National Academy of Sciences, Volume 120, Issue 11, March 2023, Pages e2214977120,
doi.org/10.1073/pnas.2214977120

Scripts and data necessary to reproduce figures at github.com/ThibaultLatrille/AdaptaPop.

• If you use mutselomega to compute ω_∗, please cite:

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,
doi.org/10.1093/molbev/msaa265

• If you use nodemutsel to compute branch/node specific N_e and μ, or if you use nodeomega to compute branch/node specific ω and μ please cite:

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,
doi.org/10.1093/molbev/msab160

Scripts and data necessary to reproduce figures at github.com/ThibaultLatrille/MutationSelectionDrift (using BayesCode v1.0).

Authors

Nicolas Lartillot (github.com/bayesiancook), Thibault Latrille (github.com/ThibaultLatrille), Vincent Lanore (github.com/vlanore), Philippe Veber (github.com/pveber) and Nicolas Rodrigue.