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

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

(2013) M. Groussin et al.   SYSTEMATIC BIOLOGY

A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection

(2012) Philippe Lemey et al.   BIOINFORMATICS

Genome-scale coestimation of species and gene trees

(2012) B. Boussau et al.   GENOME RESEARCH

Efficient Selection of Branch-Specific Models of Sequence Evolution

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

Fast and Robust Characterization of Time-Heterogeneous Sequence Evolutionary Processes Using Substitution Mapping

(2012) Jonathan Romiguier et al.   PLoS One

Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations

(2012) Brian E. Caffrey et al.   PLoS One

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

(2012) G. J. Szollosi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate Estimation of Substitution Rates with Neighbor-Dependent Models in a Phylogenetic Context

(2012) Jean Bérard et al.   SYSTEMATIC BIOLOGY

REPRESENTING A SET OF RECONCILIATIONS IN A COMPACT WAY

(2012) CELINE SCORNAVACCA et al.   Journal of Bioinformatics and Computational Biology

Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains

(2011) Paula Tataru et al.   BMC BIOINFORMATICS

Databases of homologous gene families for comparative genomics

(2009) Simon Penel et al.   BMC BIOINFORMATICS

Empirical profile mixture models for phylogenetic reconstruction

(2008) Le Si Quang et al.   BIOINFORMATICS

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

(2008) Julien Dutheil et al.   BMC EVOLUTIONARY BIOLOGY

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

Phylogenetic mixture models for proteins

(2008) S. Q. Le et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Fast, accurate and simulation-free stochastic mapping

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

Remote access to ACNUC nucleotide and protein sequence databases at PBIL

(2007) Manolo Gouy et al.   BIOCHIMIE