flalign is part of the fasta package.

PLALIGN (flalign) finds the best local alignments between two sequences.

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]