plalign is part of the fasta2 package. FASTA contains many programs for searching DNA and protein databases and for evaluating statistical significance from randomly shuffled sequences.

While programs such as fasta and ssearch report only the best alignment between the query sequence and the library sequence, lalign and plalign will report a specified number of alignments (the default is 10) between the two sequences. lalign shows the actual local alignments between the two sequences and their scores. plalign produces a plot of the alignments that looks similar to a `dot-matrix' homology plot. See also lfasta and plfasta.

References:
Pearson, W.R. Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol. 2000;132:185-219 [Entrez]

Pearson, W.R. Empirical statistical estimates for sequence similarity searches. J Mol Biol. 1998 Feb 13;276(1):71-84 [Entrez]

Pearson WR, Wood T, Zhang Z, Miller W. Comparison of DNA sequences with protein sequences. Genomics. 1997 Nov 15;46(1):24-36. [Entrez]