Estimating phylogenetic trees from pairwise likelihoods and posterior probabilities of substitution counts

DOI10.1016/J.JTBI.2011.04.005MaRDI QIDQ1783523zbMATH OpenOpenAlexWikidataFDO

Authors Mark Holder, Mike Steel

Publication date 21 September 2018

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

Full work available at URL https://doi.org/10.1016/j.jtbi.2011.04.005

zbMATH Keywords

consistencymaximum likelihoodphylogenetic inferencecounting processesdistance-based phylogenetic inference

Mathematics Subject Classification ID

Genetics and epigenetics (92D10) Problems related to evolution (92D15)

Recommendations

• Links between maximum likelihood and maximum parsimony under a simple model of site substitution
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Cites work

• scientific article; zbMATH DE number 1945176 (Why is no real title available?)
• scientific article; zbMATH DE number 5274215 (Why is no real title available?)
• A molecular sequence metric and evolutionary trees
• Counting labeled transitions in continuous-time Markov models of evolution
• Full reconstruction of Markov models on evolutionary trees: identifiability and consistency.
• Retractions of finite distance functions onto tree metrics
• The performance of neighbor-joining methods of phylogenetic reconstruction
• Toward extracting all phylogenetic information from matrices of evolutionary distances

Cited in

(8)

• Phylogenetic estimation with partial likelihood tensors
• Detection of Adaptive Shifts on Phylogenies by using Shifted Stochastic Processes on a Tree
• A basic limitation on inferring phylogenies by pairwise sequence comparisons
• Estimating the bias on the LogDeterminant transformation for evolutionary trees
• Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
• Links between maximum likelihood and maximum parsimony under a simple model of site substitution
• Improving tree probability estimation with stochastic optimization and variance reduction
• Fast likelihood calculation for multivariate Gaussian phylogenetic models with shifts

Describes a project that uses

Uses Software

• PAUP*

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