coalescentMCMC

MaRDI QIDQ7374358CRANFDO

Authors Emmanuel Paradis

Last update 23 July 2026

Copyright license GNU General Public License, version 2.0, GNU General Public License, version 3.0

Software version identifier PACKAGES.rds, 0.1, 0.2, 0.3, 0.4-1, 0.4-4, 0.4, 0.5

Description

Flexible framework for coalescent analyses in R. It includes a main function running the MCMC algorithm, auxiliary functions for tree rearrangement, and some functions to compute population genetic parameters. Extended description can be found in Paradis (2020) <doi:10.1201/9780429466700>. For details on the MCMC algorithm, see Kuhner et al. (1995) <doi:10.1093/genetics/140.4.1421> and Drummond et al. (2002) <doi:10.1093/genetics/161.3.1307>.

Cites work

• Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling.
• Estimating Mutation Parameters, Population History and Genealogy Simultaneously From Temporally Spaced Sequence Data
• Population Genomics with R

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