Site pattern probabilities under the multispecies coalescent and a relaxed molecular clock: theory and applications

DOI10.1016/j.jtbi.2022.111078zbMath1489.92109OpenAlexW4220843363MaRDI QIDQ2137445

Andrew Richards, Laura S. Kubatko

Publication date: 16 May 2022

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jtbi.2022.111078

zbMATH Keywords

molecular clockphylogeneticsmultispecies coalescenttree inferenceprobability modeling

Mathematics Subject Classification ID

Problems related to evolution (92D15)

Uses Software

• RAxML
• Seq-Gen
• BEAST
• ASTRAL-II
• STEM-hy
• FastTree
• Quartets MaxCut

Cites Work

• Unnamed Item
• The coalescent
• A supertree method for rooted trees
• Phylogenetic supertrees. Combining information to reveal the tree of life
• Bayesian-weighted triplet and quartet methods for species tree inference
• Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites
• Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent

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