Citations

• 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 the 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 the 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 the figures at github.com/ThibaultLatrille/MutationSelectionDrift (please use BayesCode v1.0).