SeqALib: A Library for Sequence Alignment

SeqALib contains efficient implementation of sequence alignment algorithms from Bioinformatics.

Templated to allow for aligning of strings and custom objects by providing a matching function of your own design.

The algorithms currently provided by SeqALib are:

• Needleman-Wunsch
• Hirschberg
• Smith-Waterman
• Gotoh Local and Global
• Myers and Miller
• BLAST (pairwise)
• FOGSAA
• MUMMER
• Suffix Trees

AUTHOR: Rodrigo Rocha and Sean Stirling

Easy to use

See full example in the file: include/Test.cpp

  std::string seq1 = "AAAGAATGCAT";
  std::string seq2 = "AAACTCAT";

  NeedlemanWunschSA<std::string,char,'-'> SA(ScoringSystem(-1,2));
  AlignedSequence<char,'-'> Alignment = SA.getAlignment(seq1,seq2);

  // The resultng Alignment contains:
  // AAA GAATGCAT
  // |||    | |||
  // AAAC   T CAT

Coming Soon

Multiple Sequence Alignment