The MAVID program uses the constrained progressive alignment ideas of Myers & Miller to do whole-genome alignment, using for constraints a gene orthology map (typically created by the Mercator program).
- Download: http://bio.math.berkeley.edu/mavid/download/
- Webserver: http://baboon.math.berkeley.edu/mavid/
- Bray & Pachter: MAVID: constrained ancestral alignment of multiple sequences. Genome Res. 2004;14:693-9.
See Mercator Perl for a tutorial on related Perl scripts.