Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs

Auch, 2010, Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison., Stand Genomic Sci, 2, 117, 10.4056/sigs.531120

Altschul, 1990, Basic local alignment search tool., J Mol Biol, 215, 403, 10.1016/S0022-2836(05)80360-2

Kent, 2002, BLAT – the BLAST-like alignment tool., Genome Res, 12, 656, 10.1101/gr.229202. Article published online before March 2002

Schwartz, 2003, Human-mouse alignments with BLASTZ., Genome Res, 13, 103, 10.1101/gr.809403

Kurtz, 2004, Versatile and open software for comparing large genomes., Genome Biol, 5, R12, 10.1186/gb-2004-5-2-r12

Moreno-Hagelsieb, 2008, Choosing BLAST options for better detection of orthologs as reciprocal best hits., Bioinformatics, 24, 319, 10.1093/bioinformatics/btm585

Henz, 2005, Whole-genome prokaryotic phylogeny., Bioinformatics, 21, 2329, 10.1093/bioinformatics/bth324

Delgado-Friedrichs, 2003, A meta-viewer for biomolecular data., GI Jahrestagung, 1, 375

Auch, 2006, Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences., BMC Bioinformatics, 7, 350, 10.1186/1471-2105-7-350

The R project for Statistical Computing. http://www.r-project.org.

Klenk, En route to a genome-based classification of Archaea and Bacteria?, Syst Appl Microbiol