Reversible polymorphism-aware phylogenetic models and their application to tree inference

DOI10.1016/j.jtbi.2016.07.042zbMath1344.92117OpenAlexW2952596786WikidataQ39536709 ScholiaQ39536709MaRDI QIDQ309245

Bui Quang Minh, Arndt von Haeseler, Dominik Schrempf, Nicola De Maio, Carolin Kosiol

Publication date: 7 September 2016

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

Full work available at URL: https://doi.org/10.1016/j.jtbi.2016.07.042

zbMATH Keywords

incomplete lineage sortingphylogeneticsreversible polymorphism-aware phylogenetic modelspecies treesubstitution model

Mathematics Subject Classification ID

Problems related to evolution (92D15) Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Genetics and epigenetics (92D10)

Related Items (3)

An alternative derivation of the stationary distribution of the multivariate neutral Wright-Fisher model for low mutation rates with a view to mutation rate estimation from site frequency data ⋮ Inference in population genetics using forward and backward, discrete and continuous time processes ⋮ Consistency and identifiability of the polymorphism-aware phylogenetic models

Uses Software

• PHYLIP
• MrBayes
• RAxML
• IQ-TREE
• SimPhy

Cites Work

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• Line-of-descent and genealogical processes, and their applications in population genetics models
• The coalescent
• On the number of segregating sites in genetical models without recombination
• Mathematical population genetics. I: Theoretical introduction.
• The allele-frequency spectrum in a decoupled Moran model with mutation, drift, and directional selection, assuming small mutation rates
• Probability Models for DNA Sequence Evolution
• Markov Chains
• Diffusion models in population genetics
• The Differential Equation of the Distribution of Gene Frequencies

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