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MODELTEST: testing the model of DNA substitution
SUMMARY The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. AVAILABILITY The MODELTEST package, including the source code and someExpand
jModelTest: phylogenetic model averaging.
  • D. Posada
  • Biology, Medicine
  • Molecular biology and evolution
  • 1 July 2008
TLDR
jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" that implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion", the "Bayesian information criterion," and a "decision-theoretic performance-based" approach. Expand
jModelTest 2: more models, new heuristics and parallel computing
jModelTest 2: more models, new heuristics and parallel computing Diego Darriba, Guillermo L. Taboada, Ramón Doallo and David Posada Supplementary Table 1. New features in jModelTest 2 SupplementaryExpand
Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests.
TLDR
It is argued that the most commonly implemented model selection approach, the hierarchical likelihood ratio test, is not the optimal strategy for model selection in phylogenetics, and that approaches like the Akaike Information Criterion (AIC) and Bayesian methods offer important advantages. Expand
ProtTest: selection of best-fit models of protein evolution
TLDR
This work has built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment in order to study protein evolution and phylogenetic inference. Expand
GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes
TLDR
GeoDis is a computer program that implements the cladistic nested analysis in which population structure can be separated from population history when it is assessed through rigorous and objective statistical tests upon an estimated nested cladogram. Expand
ProtTest 3: fast selection of best-fit models of protein evolution
TLDR
A high-performance computing (HPC) version of ProtTest that can be executed in parallel in multicore desktops and clusters, called ProtTest 3, includes new features and extended capabilities. Expand
RDP3: a flexible and fast computer program for analyzing recombination
TLDR
RDP3 is a new version of the RDP program for characterizing recombination events in DNA-sequence alignments that includes four new recombination analysis methods, new tests for recombination hot-spots, and a range of matrix methods for visualizing over-all patterns of recombination within datasets and recombination-aware ancestral sequence reconstruction. Expand
Selecting the best-fit model of nucleotide substitution.
TLDR
It is shown here that a best-fit model can be readily identified and should be routine in any phylogenetic analysis that uses models of evolution. Expand
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