[Bioperl-l] Annotation-assisted (and/or BLAST assisted) multiple sequence alignment tool?

[Brian Foley]

>From another group, I got an answer.  The MAUVE genome alignment software 
is supposed to solve this problem.
http://gel.ahabs.wisc.edu/mauve/<https://mymail.lanl.gov/owa/redir.aspx?C=5MxmGridb0ak3GxBPlpBrluXIodTEdAI9j8xfa_Xby8mfUgaFDgvWrOafUfQzPWBp5UkseJs_kU.&URL=mailto%3aweihuamian%40gmail.com>
I have not yet downloaded it and tested it, but it does seem to be the 
right tool for the job.