Tool for identifying synteny blocks among multiple pathogenomes?

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Stephen R. Doyle Popular answer

Check out Mauve. Worked well for my whole bacterial genome-by-genome work

http://genome.cshlp.org/content/14/7/1394.full

Stephen R. Doyle

Roy Ronen

Also check out Sibelia. It is fast & accurate, and can work with multiple strains/genomes at a time.

http://seqanswers.com/wiki/Sibelia

https://github.com/bioinf/Sibelia

http://bioinf.spbau.ru/sibelia

Sandeep Telkar

Thank you Stephan and Roy. Sibelia seems to be more interactive than Mauve as I have used Mauve earlier.

Axel Mosig

You may also refer to BBH-LS by Hon-Wai Leong

http://www.biomedcentral.com/1752-0509/6/S1/S22

(possibly consider contacting Hon-Wai, who is around on RG).