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BayesCode v1.3.3

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@ThibaultLatrille ThibaultLatrille released this 16 Jan 09:30
· 1 commit to chronogram since this release
v1.3.3
359f788

Site-specific adaptive evolution

Mutation-Selection framework for detecting site-specific adaptive evolution and estimating amino-acid fitness profiles as in Rodrigue et al (2021), Latrille et al (2023), Latrille et al (2024):

  • mutselomega (run the MCMC)
  • readmutselomega (read the trace).

Inferring long-term effective population size

Mutation-Selection framework for inferring changes in effective population size (Ne), mutation rate (μ) and strength of selection (ω) as in Latrille et al (2021):

  • nodemutsel (run the MCMC)
  • readnodemutsel (read the trace to obtain estimate of Ne and μ).
  • nodeomega (run the MCMC)
  • readnodeomega (read the trace to obtain estimate of ω and μ).

Detecting diversifying selection on a trait

Detecting diversifying selection for a trait from within and between-species genotypes and phenotypes as in Latrille et al (2024)

  • nodetraits (run the MCMC)
  • readnodetraits (read the trace to estimate σB, σW, ρ=σB/σW and P[ρ>1]).

Changelogs

Changelog v1.3.2→v1.3.3:

  • ⚠️ Fix issue in read of covariance matrix in readnodeomega, nodemutsel andreadnodetraits (covariance matrice could have negative variance)
  • The option --cov in read (readnodeomega, nodemutsel andreadnodetraits) also output several matrices: covariances, correlation coefficients, posterior probabilities of a positive coefficient, precisions, partial correlation coefficients, posterior probabilities of a positive partial coefficient.

Changelog v1.3.0→v1.3.2:

  • ⚠️ Fix issue in read of nucleotide mutation matrix in readomegamutsel .

Changelog v1.2.2→v1.3.0:

  • ⚠️ Fix issue in computation of ω0 in readomegamutsel .

Changelog v1.1.6→v1.2.2:

  • Added nodeomega, readnodeomega for estimating changes in ω.
  • Added nodetraits, readnodetraits for detecting diversifying selection on a trait.
  • Remove unnecessary aafitness folder
  • Can use --output argument in read to specify the output file
  • read without any argument will produce posterior mean and var

Changelog v1.0.0→v1.1.6:

  • change binaries folder from _build to bin
  • read covariance matrix
  • read annotated trees in natural space
  • scripts to plot trees and format input data (calibrations and traits)
  • updated README
  • added License
  • can compile in tiny mode (only mutselomega & nodemutsel)
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