Phylogeny estimation: traditional and Bayesian approaches
The construction of evolutionary trees is now a standard part of exploratory sequence
analysis. Bayesian methods for estimating trees have recently been proposed as a faster …
analysis. Bayesian methods for estimating trees have recently been proposed as a faster …
Potential applications and pitfalls of Bayesian inference of phylogeny
Only recently has Bayesian inference of phylogeny been proposed. The method is now a
practical alternative to the other methods; indeed, the method appears to possess …
practical alternative to the other methods; indeed, the method appears to possess …
Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests
Abstract Model selection is a topic of special relevance in molecular phylogenetics that
affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental …
affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental …
Automated phylogenetic detection of recombination using a genetic algorithm
The evolution of homologous sequences affected by recombination or gene conversion
cannot be adequately explained by a single phylogenetic tree. Many tree-based methods for …
cannot be adequately explained by a single phylogenetic tree. Many tree-based methods for …
Species Delimitation Using Bayes Factors: Simulations and Application to the Sceloporus scalaris Species Group (Squamata: Phrynosomatidae)
Current molecular methods of species delimitation are limited by the types of species
delimitation models and scenarios that can be tested. Bayes factors allow for more flexibility …
delimitation models and scenarios that can be tested. Bayes factors allow for more flexibility …
The inference of gene trees with species trees
This article reviews the various models that have been used to describe the relationships
between gene trees and species trees. Molecular phylogeny has focused mainly on …
between gene trees and species trees. Molecular phylogeny has focused mainly on …
Leptospira interrogans Endostatin-Like Outer Membrane Proteins Bind Host Fibronectin, Laminin and Regulators of Complement
B Stevenson, HA Choy, M Pinne, ML Rotondi… - PloS one, 2007 - journals.plos.org
The pathogenic spirochete Leptospira interrogans disseminates throughout its hosts via the
bloodstream, then invades and colonizes a variety of host tissues. Infectious leptospires are …
bloodstream, then invades and colonizes a variety of host tissues. Infectious leptospires are …
Estimating diversifying selection and functional constraint in the presence of recombination
DJ Wilson, G McVean - Genetics, 2006 - academic.oup.com
Abstract Models of molecular evolution that incorporate the ratio of nonsynonymous to
synonymous polymorphism (d N/d S ratio) as a parameter can be used to identify sites that …
synonymous polymorphism (d N/d S ratio) as a parameter can be used to identify sites that …
Molecular evolution and mosaicism of leptospiral outer membrane proteins involves horizontal DNA transfer
Leptospires belong to a genus of parasitic bacterial spirochetes that have adapted to a
broad range of mammalian hosts. Mechanisms of leptospiral molecular evolution were …
broad range of mammalian hosts. Mechanisms of leptospiral molecular evolution were …
Dual multiple change-point model leads to more accurate recombination detection
Motivation: We introduce a dual multiple change-point (MCP) model for recombination
detection among aligned nucleotide sequences. The dual MCP model is an extension of the …
detection among aligned nucleotide sequences. The dual MCP model is an extension of the …