lfasta 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.

lfasta uses the fasta algorithm and should be chosen over lalign for aligning long sequences. For aligning peptides, see also lalign and plalign.

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]