ModelOMatic: Fast and Automated Model Selection between RY, Nucleotide, Amino Acid, and Codon Substitution Models

Assessing the State of Substitution Models Describing Noncoding RNA Evolution

(2014) James E. Allen et al.   Genome Biology and Evolution

Detection of Implausible Phylogenetic Inferences Using Posterior Predictive Assessment of Model Fit

(2014) Jeremy M. Brown   SYSTEMATIC BIOLOGY

CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models

(2013) Manuel Gil et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

(2012) Ylenia Chiari et al.   BMC BIOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Molecular phylogenetics: principles and practice

(2012) Ziheng Yang et al.   NATURE REVIEWS GENETICS

The interface of protein structure, protein biophysics, and molecular evolution

(2012) David A. Liberles et al.   PROTEIN SCIENCE

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Potential pitfalls of modelling ribosomal RNA data in phylogenetic tree reconstruction: Evidence from case studies in the Metazoa

(2011) Harald O Letsch et al.   BMC EVOLUTIONARY BIOLOGY

Markovian and Non-Markovian Protein Sequence Evolution: Aggregated Markov Process Models

(2011) Carolin Kosiol et al.   JOURNAL OF MOLECULAR BIOLOGY

MISFITS: Evaluating the Goodness of Fit between a Phylogenetic Model and an Alignment

(2010) Minh Anh Thi Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences

(2010) Jerome C. Regier et al.   NATURE

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION

An Improved General Amino Acid Replacement Matrix

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

The genetic code can cause systematic bias in simple phylogenetic models

(2008) S. Whelan   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Synonymous Substitutions Substantially Improve Evolutionary Inference from Highly Diverged Proteins

(2008) Tae-Kun Seo et al.   SYSTEMATIC BIOLOGY