MAVID

MAVID is a multiple alignment program that is suitable for alignments of large numbers of DNA sequences. The sequences can be small mitochondrial genomes or large genomic regions up to megabases long. MAVID is also integrated with various phlogenetic tree construction programs, conservation identification, and visualization tools, and can be used to identify conserved regions in phylogenetically related sequences. It is important to note that MAVID is currently a DNA sequence alignment program and cannot align protein sequences. MAVID is a progressive alignment algorithm. Maximum likelihood estimates of the ancestral sequences are aligned recursively using the AVID pairwise alignment method. AVID is a hierarchical alignment algorithm which works by iteratively aligning large anchors, finally aligning weakly conserved regions using the Smith-Waterman algorithm.

MAVID has been used to align verteberate genomic sequences, mitochondrial DNA, viruses, and other sequences. MAVID is not currently well suited to aligning sequences where global alignment is not necessarily biologically meaningful (for example because of rearrangements or inversion). A more appropriate tool at this time for such alignments is E. coli Blast.