Improving Phylogenetic Inference with a Semiempirical Amino Acid Substitution Model

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

(2012) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

A New Semiempirical Codon Substitution Model Based on Principal Component Analysis of Mammalian Sequences

(2011) S. Zoller et al.   MOLECULAR BIOLOGY AND EVOLUTION

Non-Negative Matrix Factorization for Learning Alignment-Specific Models of Protein Evolution

(2011) Ben Murrell et al.   PLoS One

Empirical Analysis of the Most Relevant Parameters of Codon Substitution Models

(2010) Stefan Zoller et al.   JOURNAL OF MOLECULAR EVOLUTION

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

(2010) Si Quang Le et al.   SYSTEMATIC BIOLOGY

Support Patterns from Different Outgroups Provide a Strong Phylogenetic Signal

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

Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets

(2008) Arjun B. Prasad et al.   MOLECULAR BIOLOGY AND EVOLUTION

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