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ALP

ALP

ALP (Ascending Ladder Program) is a tool to calculate the statistical parameters in the modified Gumbel distribution for BLAST. The ALP algorithm computes E-values for random local DNA-DNA and protein-protein alignments, gap costs, and character abundances for any substitution matrix. FALP (Frameshift Ascending Ladder Program) is a tool for comparable tasks for frameshifting DNA-protein alignments. The tools are available as a library or a standalone implementation.

Topic

Nucleic acid structure analysis; Statistics and probability; Genomics

Details

  • Operation: Statistical calculation
  • Software interface: Graphical user interface; Library
  • Language: C++
  • Operating system: Linux; Microsoft Windows
  • License: Public domain
  • Cost: Free
  • Version name: 1.98
  • Maturity: Mature
  • Credit: The Intramural Research Program of the National Institutes of Health, National Library of Medicine, and National Center for Biotechnology Information, KAKENHI.
  • Contact: spouge _at_ ncbi.nlm.nih.gov
  • Collection: -

Publications

Sheetlin S, Park Y, Frith MC, Spouge JL "ALP & FALP: C++ libraries for pairwise local alignment E-values." Bioinformatics 2016; 32(2):304-5 https://doi.org/10.1093/bioinformatics/btv575
PMID: 26428291
PMCID: PMC4739181


Sheetlin SL, Park Y, Frith MC, Spouge JL "Frameshift alignment: statistics and post-genomic applications." Bioinformatics, 2014 https://doi.org/10.1093/bioinformatics/btu576
PMID: 25172925
PMCID: PMC4253828


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