Mugsy: fast multiple alignment of closely related whole genomes

A min-cut algorithm for the consistency problem in multiple sequence alignment

(2010) E. Corel et al.   BIOINFORMATICS

Comparative assessment of methods for aligning multiple genome sequences

(2010) Xiaoyu Chen et al.   NATURE BIOTECHNOLOGY

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

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

The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group

(2009) S.-M. Ahn et al.   GENOME RESEARCH

Multiple whole-genome alignments without a reference organism

(2009) I. Dubchak et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Fast Statistical Alignment

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

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment

(2008) Benedict Paten et al.   BIOINFORMATICS

Segment-based multiple sequence alignment

(2008) T. Rausch et al.   BIOINFORMATICS

SeqAn An efficient, generic C++ library for sequence analysis

(2008) Andreas Döring et al.   BMC BIOINFORMATICS

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

(2008) B. Paten et al.   GENOME RESEARCH

A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

(2008) M. Deloger et al.   JOURNAL OF BACTERIOLOGY

The diploid genome sequence of an Asian individual

(2008) Jun Wang et al.   NATURE