Multiple Alignments with COBALT

COBALT incorporates pairwise constraints into a progressive multiple alignment.    The pairwise constraints are derived from the conserved domain database, the protein motif database, and sequence similarity searches, using RPS-BLAST, BLASTP, and PHI-BLAST
(http://www.ncbi.nlm.nih.gov/pubmed/17332019).
COBALT can be started from BLAST results (use the "Multiple Alignment" link) or from the COBALT web site at http://www.ncbi.nlm.nih.gov/tools/cobalt/cobalt.cgi?CMD=Web