Assessing the State of Substitution Models Describing Noncoding RNA Evolution

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

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

MicroRNA evolution by arm switching

(2011) Sam Griffiths-Jones et al.   EMBO REPORTS

Genome-Wide Heterogeneity of Nucleotide Substitution Model Fit

(2011) Leonardo Arbiza et al.   Genome Biology and Evolution

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

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

Evolution of microRNA diversity and regulation in animals

(2011) Eugene Berezikov   NATURE REVIEWS GENETICS

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Molecular evidence for a diverse green algal community growing in the hair of sloths and a specific association with Trichophilus welckeri (Chlorophyta, Ulvophyceae)

(2010) Milla Suutari et al.   BMC EVOLUTIONARY BIOLOGY

Rfam: Wikipedia, clans and the "decimal" release

(2010) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Nearly complete rRNA genes assembled from across the metazoan animals: Effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction

(2009) Jon Mallatt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

The Genetic Signatures of Noncoding RNAs

(2009) John S. Mattick   PLoS Genetics

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment

(2008) Benedict Paten et al.   BIOINFORMATICS

Strategies for measuring evolutionary conservation of RNA secondary structures

(2008) Andreas R Gruber et al.   BMC BIOINFORMATICS

Genome-wide nucleotide-level mammalian ancestor reconstruction

(2008) B. Paten et al.   GENOME RESEARCH

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   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