Model selection in phylogenetics
▪ Abstract Investigation into model selection has a long history in the statistical literature. As
model-based approaches begin dominating systematic biology, increased attention has …
model-based approaches begin dominating systematic biology, increased attention has …
Using PhyloSuite for molecular phylogeny and tree‐based analyses
Phylogenetic analysis has entered the genomics (multilocus) era. For less experienced
researchers, conquering the large number of software programs required for a multilocus …
researchers, conquering the large number of software programs required for a multilocus …
Model use in phylogenetics: nine key questions
Models of character evolution underpin all phylogeny estimations, thus model adequacy
remains a crucial issue for phylogenetics and its many applications. Although progress has …
remains a crucial issue for phylogenetics and its many applications. Although progress has …
Model selection may not be a mandatory step for phylogeny reconstruction
Determining the most suitable model for phylogeny reconstruction constitutes a fundamental
step in numerous evolutionary studies. Over the years, various criteria for model selection …
step in numerous evolutionary studies. Over the years, various criteria for model selection …
[LLIBRE][B] Modern phylogenetic comparative methods and their application in evolutionary biology: concepts and practice
LZ Garamszegi - 2014 - Springer
Many evolutionary biologists are concerned with the tremendous amount of diversity of
species, and their phenotypes, that we can currently observe in nature, and one of the most …
species, and their phenotypes, that we can currently observe in nature, and one of the most …
jModelTest: phylogenetic model averaging
D Posada - Molecular biology and evolution, 2008 - academic.oup.com
Abstract jModelTest is a new program for the statistical selection of models of nucleotide
substitution based on “Phyml”(. A simple, fast, and accurate algorithm to estimate large …
substitution based on “Phyml”(. A simple, fast, and accurate algorithm to estimate large …
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
Background In recent years, model based approaches such as maximum likelihood have
become the methods of choice for constructing phylogenies. A number of authors have …
become the methods of choice for constructing phylogenies. A number of authors have …
Mitochondrial introgression and incomplete lineage sorting through space and time: phylogenetics of crotaphytid lizards
We investigate the roles of mitochondrial introgression and incomplete lineage sorting
during the phylogenetic history of crotaphytid lizards. Our Bayesian phylogenetic estimate …
during the phylogenetic history of crotaphytid lizards. Our Bayesian phylogenetic estimate …
Phylogenetic systematics and biogeography of hummingbirds: Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate …
Hummingbirds are an important model system in avian biology, but to date the group has
been the subject of remarkably few phylogenetic investigations. Here we present partitioned …
been the subject of remarkably few phylogenetic investigations. Here we present partitioned …
Selection of Models of DNA Evolution with jModelTest
D Posada - Bioinformatics for DNA sequence analysis, 2009 - Springer
Abstract jM odel T est is a bioinformatic tool for choosing among different models of
nucleotide substitution. The program implements five different model selection strategies …
nucleotide substitution. The program implements five different model selection strategies …