MSA
MSA is a program to perform multiple sequence alignment under the sum-of-pairs criterion. This means that the cost of a multiple alignment of n sequences is the sum of the n choose 2 costs of the implicit pairwise alignments. By default, MSA implements a weighted sum algorithm, where the weights are computed using the method in: Altschul SF, Carroll RJ, Lipman DJ. (1989) "Weights for data related by a tree" J Mol Biol 207:647-653; Altschul SF(1989) "Leaf pairs and tree dissections" SIAM J Discrete Math 2:293-299.If you want to be on the MSA mailing list at NCBI or have comments, questions, or suggestions on MSA, send mail to Alejandro Schäffer.
Lipman, DJ, Altschul, S, and Kececioglu, J (1989) A tool for multiple sequence alignment. PNAS USA. 86:4412-4415.
Manual: http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/msa.html
INPUT = Protein or DNA sequences.