PAT - Protein Alignment Tool

References

1. MACAW: a workbench for multiple alignment construction and analysis, Schuler GD, Altschul SF, Lipman DJ, Proteins. 1991; 9(3): 180-90

2. AL2CO: calculation of positional conservation in a protein sequence alignment, Jimin Pei and Nick V. Grishin, Bioinformatics. 2001 Aug; 17(8): 700-712

3. Position-based sequence weights, Steven Henikoff and Jorja G. Henikoff, J Mol Biol. 1994 Nov 4; 243(4): 574-8