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SeqALib: Sequence Alignment Library

License: Apache License 2.0

C++ 99.80% Makefile 0.20%

bioinformatics sequence-alignment software-library covid19 covid-19

seqalib's Introduction

SeqALib: A Library for Sequence Alignment

SeqALib contains efficient implementation of sequence alignment algorithms from Bioinformatics.

The algorithms currently provided by SeqALib are:

AUTHOR: Rodrigo Rocha and Sean Stirling

Easy to use

See full example in the file: test/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

seqalib's People

Contributors

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seanst98 zeta1999

seqalib's Issues

Licensing

This is an interesting repository which could be useful for research - I'll note that the use of templates may give the repository wider applicability than some others: there are some use cases for sequence alignment outside of bioinformatics, but the alphabet in such cases is not DNA bases and can be arbitrarily large.

However, it is unfortunately illegal to make use of your repository currently, as you have not licensed it (and therefore all rights are reserved).

If you would like to attach a license, GitHub offers some guidance: https://help.github.com/en/github/creating-cloning-and-archiving-repositories/licensing-a-repository

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