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MSA software

This page describes the software package MSA to compute multiple sequence alignments of biological sequences. The MSA software package was originally developed by Stephen Altschul, John Kececioglu, and David Lipman, and is described in:

• Lipman DJ, Altschul SF, Kececioglu JD. A tool for multiple sequence alignment. Proc Natl Acad Sci USA. 1989; 86:4412-4415. [PubMed]

• Gupta SK, Kececioglu J, Schäffer AA. Improving the practical space and time efficiency of the shortest-paths Approach to sum-of-pairs multiple sequence alignment. J Comput. Biol 1995; 2:459-472. [PubMed] [paper.ps]

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. Weights for data related by a tree. J Mol Biol. 1989; 207:647-653. [PubMed]
  
  
• Altschul SF. Leaf pairs and tree dissections. SIAM J Discrete Math. 1989; 2:293-299.

MSA is designed to run under the UNIX operating system and generally requires several megabytes of memory. The form that input to the program is required to take is described on the original manual page that comes with the software.

There is an MSA mailing list for those who wish to learn about bugs and updates. If you want to be on the MSA mailing list or have comments, questions, or suggestions on MSA, send mail to Alejandro Schäffer.