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

BioTorrents: A File Sharing Service for Scientific Data

(2010) Morgan G. I. Langille et al.   PLoS One

Multiple whole-genome alignments without a reference organism

(2009) I. Dubchak et al.   GENOME RESEARCH

A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats

(2009) T.J. Treangen et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Simultaneous Bayesian gene tree reconstruction and reconciliation analysis

(2009) O. Akerborg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast Statistical Alignment

(2009) Robert K. Bradley et al.   PLoS Computational Biology

Inferring genomic flux in bacteria

(2008) X. Didelot et al.   GENOME RESEARCH

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

(2008) B. Paten et al.   GENOME RESEARCH

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

Multi-Break Rearrangements and Breakpoint Re-Uses: From Circular to Linear Genomes

(2008) Max A. Alekseyev   JOURNAL OF COMPUTATIONAL BIOLOGY

The infinite sites model of genome evolution

(2008) J. Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics of Genome Rearrangement in Bacterial Populations

(2008) Aaron E. Darling et al.   PLoS Genetics

Uncertainty in homology inferences: Assessing and improving genomic sequence alignment

(2007) G. Lunter et al.   GENOME RESEARCH