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chronos: Molecular Dating by Penalised Likelihood and Maximum Likelihood


Confidence intervals in molecular dating by penalised likelihood

Installation


install.packages("devtools");
devtools::install_github("josephwb/chronos", dependencies=TRUE);

References


Claramunt S, Cracraft J. 2015. A new time tree reveals Earth history’s imprint on the evolution of modern birds. Science Advances, 1(11), e1501005. doi: 10.1126/sciadv.1501005.

Kim, J., Sanderson, M. J. 2008. Penalized likelihood phylogenetic inference: bridging the parsimony-likelihood gap. Systematic Biology 57(5): 665–674. doi: 10.1080/10635150802422274

Paradis, E. 2013. Molecular dating of phylogenies by likelihood methods: a comparison of models and a new information criterion. Molecular Phylogenetics and Evolution 67(2): 436–444. doi: 10.1016/j.ympev.2013.02.008

Paradis, E., Schliep, K. 2019. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35(3): 526-528. doi: 10.1093/bioinformatics/bty633

Sanderson, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution 19(1): 101–109. doi: 10.1093/oxfordjournals.molbev.a003974

Schliep, K. P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics 27(4): 592-593. doi: 10.1093/bioinformatics/btq706

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