Modeling Protein Evolution with Several Amino Acid Replacement Matrices Depending on Site Rates

Accounting for Solvent Accessibility and Secondary Structure in Protein Phylogenetics Is Clearly Beneficial

(2010) Si Quang Le 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

Empirical profile mixture models for phylogenetic reconstruction

(2008) Le Si Quang et al.   BIOINFORMATICS

A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

(2008) Huai-Chun Wang et al.   BMC EVOLUTIONARY BIOLOGY

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le 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

A Justification for Reporting the Majority-Rule Consensus Tree in Bayesian Phylogenetics

(2008) Mark T. Holder et al.   SYSTEMATIC BIOLOGY