COBALT tool for multiple protein sequence alignment

The Constrain-Based Alignment Tool (COBALT) aligns multiple protein
sequences. The program uses amino acid frequencies from conserved domain
database (CDD) and collection of pairwise constraints derived
from CDD, protein motifs, and local sequence similarity using RPS-BLAST,
BLASTP, and PHI-BLAST. The constraints are incorporated into the multiple
alignment.

References
Papadopoulos JS and Agarwala R (2007) COBALT: constraint-based alignment
tool for multiple protein sequences, Bioinformatics 23, 1073--1079

See also:
http://www.ncbi.nlm.nih.gov/tools/cobalt
