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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
ALP & FALP: C++ libraries for pairwise local alignment E-values
Sergey Sheetlin1, Yonil Park1, Martin C Frith2
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, MD 20894, USA and.
Motivation:
Pairwise local alignment is an indispensable tool for molecular biologists. In real time (i.e. in about 1 s), ALP (Ascending Ladder Program) calculates the E-values for protein-protein or DNA-DNA local alignments of random sequences, for arbitrary substitution score matrix, gap costs and letter abundances; and FALP (Frameshift Ascending Ladder Program) performs a similar task, although more slowly, for frameshifting DNA-protein alignments.
Availability And Implementation:
To permit other C++ programmers to implement the computational efficiencies in ALP and FALP directly within their own programs, C++ source codes are available in the public domain at http://go.usa.gov/3GTSW under 'ALP' and 'FALP', along with the standalone programs ALP and FALP.
Contact:
spouge@nih.gov
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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