MAVID is a multiple alignment program suitable for many large genomic regions. The MAVID allows biomedical researchers to quickly obtain multiple alignments for genomic sequences and to subsequently analyse the alignments for conserved regions. MAVID has been successfully used for the alignment of closely related species such as primates and also for the alignment of more distant organisms such as human and fugu.
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N. Bray and L. Pachter,
MAVID: Constrained ancestral alignment of multiple sequences
Genome Research, 14:693-699 (2004).