The FSA multiple alignment server

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

Submit DNA, RNA or protein sequences file (multi-FASTA text file):  
Email address to notify when results are ready:  

Sequences must be submitted as plain text files (MS Word documents, etc., are not permissible).


Gap factor:
Model type:

Due to computational constraints, we cannot process alignments of more than 10 megabases of sequence or of more than 100 sequences.
Please download FSA if you wish to create such alignments. If you wish to align long sequences (> 10 kilobases), then we strongly recommend that you download FSA and use it in conjunction with the exonerate homology-search tool.

If you use FSA, please cite:

Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L (2009) Fast Statistical Alignment. PLoS Computational Biology. 5:e1000392.

The server is currently running FSA version 1.15.2. The software is distributed under the GNU General Public License (GPL) and the source code is available for download.
If you have questions about FSA please see the FAQ page, or email

This site is under development.