MSA is a global multiple sequence alignment program that aligns several protein or nucleic acid sequences. It will produce a heuristic alignment and an optimal alignment, if one exists. It will also calculate the alignment cost, the epsilons for each pairwise alignment, and the maximum score of an optimal alignment.

Installed on the Opteron Cluster.

MSA users will find it convenient to use the /biomed/lib/examples/.login.fixed login file. It adds to your default path directories where many sequence analysis packages are stored, sets up the environment for EMBOSS, and defines some environment variables for sequence analysis packages.

Opteron version:

• version 2.1, PSC revision b
• Usage, Up to 50 sequences, each sequence has < 150 residues:

  /biomed/bin/msa_50_150

  Up to 25 sequences, each sequence has < 500 residues:

  /biomed/bin/msa_25_500

  Up to 10 sequences, each sequence has < 1000 residues:

  /biomed/bin/msa_10_1000

• Examples

Other MSA documentation:

• Sequence analysis tutorials developed at PSC.
• MSA User's Guide, version 2.1, revision b.

See also:

• Other nucleic acid and protein sequence analysis packages installed at the PSC.