Estimating Empirical Codon Hidden Markov Models

Tools for simulating evolution of aligned genomic regions with integrated parameter estimation

(2012) Avinash Varadarajan et al.   GENOME BIOLOGY

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

Pervasive Multinucleotide Mutational Events in Eukaryotes

(2011) Daniel R. Schrider et al.   CURRENT BIOLOGY

Positive Selection Differs between Protein Secondary Structure Elements in Drosophila

(2010) Kate E. Ridout et al.   Genome Biology and Evolution

Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles

(2010) N. Rodrigue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences

(2010) Wayne Delport et al.   PLoS Computational Biology

Accurate Estimation of Gene Evolutionary Rates Using XRATE, with an Application to Transmembrane Proteins

(2009) A. Heger et al.   MOLECULAR BIOLOGY AND EVOLUTION

Statistical Comparison of Nucleotide, Amino Acid, and Codon Substitution Models for Evolutionary Analysis of Protein-Coding Sequences

(2009) Tae-Kun Seo et al.   SYSTEMATIC BIOLOGY

Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models

(2008) M. Anisimova et al.   MOLECULAR BIOLOGY AND EVOLUTION