Selectome update: quality control and computational improvements to a database of positive selection

The Branch-Site Test of Positive Selection Is Surprisingly Robust but Lacks Power under Synonymous Substitution Saturation and Variation in GC

(2013) Walid H. Gharib et al.   MOLECULAR BIOLOGY AND EVOLUTION

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm

(2012) Ari Löytynoja et al.   BIOINFORMATICS

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes

(2011) P. Markova-Raina et al.   GENOME RESEARCH

Evolutionary Models Accounting for Layers of Selection in Protein-Coding Genes and their Impact on the Inference of Positive Selection

(2011) N. D. Rubinstein et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

(2011) G. Jordan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving the Performance of Positive Selection Inference by Filtering Unreliable Alignment Regions

(2011) Eyal Privman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species

(2011) Paul J. Kersey et al.   NUCLEIC ACIDS RESEARCH

An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty

(2010) O. Penn et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

(2010) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for an episodic model of protein sequence evolution

(2009) Romain A. Studer et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

(2008) R. A. Studer et al.   GENOME RESEARCH

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Selectome: a database of positive selection

(2008) E. Proux et al.   NUCLEIC ACIDS RESEARCH