Sequence Context of Indel Mutations and Their Effect on Protein Evolution in a Bacterial Endosymbiont

Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist

(2012) Laura E Williams et al.   BMC GENOMICS

Accurate Reconstruction of Insertion-Deletion Histories by Statistical Phylogenetics

(2012) Oscar Westesson et al.   PLoS One

Insertions and deletions trigger adaptive walks in Drosophila proteins

(2012) E. V. Leushkin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Predicting the effects of frameshifting indels

(2012) Jing Hu et al.   GENOME BIOLOGY

Purifying Selection, Sequence Composition, and Context-Specific Indel Mutations Shape Intraspecific Variation in a Bacterial Endosymbiont

(2011) Laura E. Williams et al.   Genome 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

Reduced Selective Constraint in Endosymbionts: Elevation in Radical Amino Acid Replacements Occurs Genome-Wide

(2011) Jennifer J. Wernegreen   PLoS One

Sequence Conservation and Functional Constraint on Intergenic Spacers in Reduced Genomes of the Obligate Symbiont Buchnera

(2011) Patrick H. Degnan et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Evolution of Prokaryotic Genes by Shift of Stop Codons

(2010) Anna A. Vakhrusheva et al.   JOURNAL OF MOLECULAR 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

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

(2010) Federico Abascal et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

One nutritional symbiosis begat another: Phylogenetic evidence that the ant tribe Camponotini acquired Blochmannia by tending sap-feeding insects

(2009) Jennifer J Wernegreen et al.   BMC EVOLUTIONARY BIOLOGY

The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria

(2009) N. A. Moran et al.   SCIENCE

Genomics and Evolution of Heritable Bacterial Symbionts

(2008) Nancy A. Moran et al.   Annual Review of Genetics

Patterns and rates of nucleotide substitution, insertion and deletion in the endosymbiont of antsBlochmannia floridanus

(2008) L. GÓMEZ-VALERO et al.   MOLECULAR ECOLOGY

Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes

(2008) Dacheng Tian et al.   NATURE

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts

(2008) I. Tamas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA