Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies

How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the Fisher-Wright mutation-selection framework

(2015) M. dos Reis   Biology Letters

Advances in Computer Simulation of Genome Evolution: Toward More Realistic Evolutionary Genomics Analysis by Approximate Bayesian Computation

(2015) Miguel Arenas   JOURNAL OF MOLECULAR EVOLUTION

The Relationship between dN/dS and Scaled Selection Coefficients

(2015) Stephanie J. Spielman et al.   MOLECULAR BIOLOGY AND EVOLUTION

πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios

(2014) Filip Bielejec et al.   BMC BIOINFORMATICS

A Penalized-Likelihood Method to Estimate the Distribution of Selection Coefficients from Phylogenetic Data

(2014) Asif U. Tamuri et al.   GENETICS

Antibody-Specific Model of Amino Acid Substitution for Immunological Inferences from Alignments of Antibody Sequences

(2014) Alexander Mirsky et al.   MOLECULAR BIOLOGY AND EVOLUTION

Simulation of Genome-Wide Evolution under Heterogeneous Substitution Models and Complex Multispecies Coalescent Histories

(2014) Miguel Arenas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Protein evolution along phylogenetic histories under structurally constrained substitution models

(2013) Miguel Arenas et al.   BIOINFORMATICS

Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package

(2013) N. Rodrigue et al.   BIOINFORMATICS

REvolver: Modeling Sequence Evolution under Domain Constraints

(2012) Tina Koestler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Simulation of Molecular Data under Diverse Evolutionary Scenarios

(2012) Miguel Arenas   PLoS Computational Biology

Estimating the Distribution of Selection Coefficients from Phylogenetic Data Using Sitewise Mutation-Selection Models

(2011) A. U. Tamuri et al.   GENETICS

ALF—A Simulation Framework for Genome Evolution

(2011) Daniel A. Dalquen et al.   MOLECULAR BIOLOGY AND EVOLUTION

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

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

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage

(2008) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes

(2008) M. T Holder et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES