Distribution of distances between topologies and its effect on detection of phylogenetic recombination

DOI10.1007/S10463-009-0259-8MaRDI QIDQ904079zbMATHOpenAlexFDO

Authors Leonardo de Oliveira Martins, Hirohisa Kishino

Publication date 15 January 2016

Published in Annals of the Institute of Statistical Mathematics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/s10463-009-0259-8

zbMATH Keywords

Markov chain Monte CarlophylogeneticsSPR distanceviral recombination

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Problems related to evolution (92D15) Applications of branching processes (60J85)

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Cites work

• scientific article; zbMATH DE number 3943611 (Why is no real title available?)
• A new look at the statistical model identification
• Bayes Factors
• Bayesian Measures of Model Complexity and Fit
• Bayesian Variable Selection in Linear Regression
• Bayesian curve-fitting with free-knot splines
• Improving the acceptance rate of reversible jump MCMC proposals
• Inferring Spatial Phylogenetic Variation Along Nucleotide Sequences
• On the combinatorics of rooted binary phylogenetic trees
• Parameterization and Bayesian Modeling
• Subtree transfer operations and their induced metrics on evolutionary trees

Cited in

(7)

• Addressing the shortcomings of three recent Bayesian methods for detecting interspecific recombination in DNA sequence alignments
• Synonymous and nonsynonymous distances help untangle convergent evolution and recombination
• Distribution and asymptotic behavior of the phylogenetic transfer distance
• BIOLOGICAL DISTANCES ON DNA KNOTS AND LINKS: Applications to XER recombination
• Quantifying genetic innovation: mathematical foundations for the topological study of reticulate evolution
• Maximum likelihood estimates of pairwise rearrangement distances
• On the effect of intralocus recombination on triplet-based species tree estimation

Describes a project that uses

Uses Software

• fastDNAml
• PAML
• BayesDA
• cBrother

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