Mixture Models of Nucleotide Sequence Evolution that Account for Heterogeneity in the Substitution Process Across Sites and Across Lineages

Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics

(2014) Victor A Vera-Ruiz et al.   BMC BIOINFORMATICS

Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution

(2013) Laurent Guéguen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Searching for the optimal data partitioning strategy in mitochondrial phylogenomics: A phylogeny of Acridoidea (Insecta: Orthoptera: Caelifera) as a case study

(2013) James R. Leavitt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences

(2013) M. Groussin et al.   SYSTEMATIC BIOLOGY

Efficient Selection of Branch-Specific Models of Sequence Evolution

(2012) Julien Y. Dutheil et al.   MOLECULAR BIOLOGY AND EVOLUTION

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fitting Nonstationary General-Time-Reversible Models to Obtain Edge-Lengths and Frequencies for the Barry–Hartigan Model

(2012) Liwen Zou et al.   SYSTEMATIC BIOLOGY

Problems With Estimation of Ancestral Frequencies Under Stationary Models

(2012) Edward Susko et al.   SYSTEMATIC BIOLOGY

Reducing Model Complexity of the General Markov Model of Evolution

(2011) V. Jayaswal et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Parameters of the Barry and Hartigan General Markov Model Are Statistically NonIdentifiable

(2011) Liwen Zou et al.   SYSTEMATIC BIOLOGY

Two Stationary Nonhomogeneous Markov Models of Nucleotide Sequence Evolution

(2010) Vivek Jayaswal et al.   SYSTEMATIC BIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs

(2008) Julien Dutheil et al.   BMC EVOLUTIONARY BIOLOGY

A Site- and Time-Heterogeneous Model of Amino Acid Replacement

(2008) Samuel Blanquart et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast, accurate and simulation-free stochastic mapping

(2008) V. N Minin et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES