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

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

(2012) Laura E Williams et al.   BMC GENOMICS

Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format

(2011) M. N. Edmonson et al.   BIOINFORMATICS

Bacterial symbionts in insects or the story of communities affecting communities

(2011) J. Ferrari et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Chromosome Stability and Gene Loss in Cockroach Endosymbionts

(2010) Z. L. Sabree et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Variation in the Ratio of Nucleotide Substitution and Indel Rates across Genomes in Mammals and Bacteria

(2009) J.-Q. Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

DNAPlotter: circular and linear interactive genome visualization

(2008) T. Carver et al.   BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

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

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

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