Molecular timetrees using relaxed clocks and uncertain phylogenies

In this repository, you can find a description of the RelTime-JA method that combines the bag of little bootstraps, maximum likelihood, and RelTime approaches for simultaneously inferring evolutionary relationships, divergence times, and confidence intervals incorporating phylogeny uncertainty. You can also find the computer simulated and empirical phylogenomic datasets analyzed in this study. You can find as well a tutorial of RelTime-JA with little bootstraps method. For a more detailed explanation of the method, please read our manuscript (DOI: doi.org/10.3389/fbinf.2023.1225807).

Directory structure

• code directory contains the software, R code, and shell scripts required to carry out the RelTime-JA analyses of computer simulated and empirical phylogenomic datasets.

• data directory contains computer simulated and empirical phylogenomic datasets analyzed for this study.

• reltime-ja_tutorial directory contains a tutorial of the RelTime-JA with little bootstraps method, and software, R code, shell scripts, and data used in the tutorial.

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We hope you find this repository useful. For comments and questions please e-mail j.barba@temple.edu.