Phylomark, a Tool To Identify Conserved Phylogenetic Markers from Whole-Genome Alignments

Cyanobacterial construction of hot spring siliceous stromatolites in Yellowstone National Park

(2012) Charles Pepe-Ranney et al.   ENVIRONMENTAL MICROBIOLOGY

Making whole genome multiple alignments usable for biologists

(2011) Daniel Blankenberg et al.   BIOINFORMATICS

Obscured phylogeny and possible recombinational dormancy in Escherichia coli

(2011) Shana R Leopold et al.   BMC EVOLUTIONARY BIOLOGY

Mugsy: fast multiple alignment of closely related whole genomes

(2010) Samuel V. Angiuoli et al.   BIOINFORMATICS

Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions

(2010) Chad Laing et al.   BMC BIOINFORMATICS

A Comparative Genomic Analysis of Diverse Clonal Types of EnterotoxigenicEscherichia coliReveals Pathovar-Specific Conservation

(2010) Jason W. Sahl et al.   INFECTION AND IMMUNITY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

Segment-based multiple sequence alignment

(2008) T. Rausch et al.   BIOINFORMATICS

Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains

(2008) Françoise Jaureguy et al.   BMC GENOMICS

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY