The MAVID/AMAP multiple alignment server



We have been working on a new alignment program, called FSA, that will be replacing AMAP/MAVID in the near future. The FSA web server is now running and we encourage you to try it. FSA will align protein, DNA and RNA sequences; a key feature is that it provides detailed information at the nucleotide/amino acid level about the accuracy and uncertainty of alignments.
Download MAVID
See examples of MAVID alignments.

If you have questions about MAVID please see the user guide or FAQ page.

Enter sequences to process (at least 2 sequences required):

Submit DNA or protein sequences file (multi-FASTA text file):  
      and/or
Input list of GENBANK accession numbers (separated by spaces): TEMPORARILY DISABLED

Optional input:

Email address to notify when results are ready:


Annotation file (GAF format):
FASTA line of sequence to which annotation corresponds:


Vista plot parameters:

If you use MAVID please cite:

Bray N and Pachter L, MAVID: Constrained ancestral alignment of multiple sequences,, Genome Research, 14:693-699 (2004).
(MAVID supplementary website, AVID supplementary website)

The server is currently running MAVID version 2.0.4 and Colin Dewey's MapMaker version 0.1.
If you have questions or comments please email Nicolas Bray and Lior Pachter.

Amino acid alignments are being performed with AMAP version 2.0. Please see the AMAP website for documentation and citation information.

The site was last updated on April 14, 2006.