|MSA Package for Multiple Sequence Alignment|
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:
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:
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.