sequence-alignment

A simple Java package for sequence alignment and scoring.

In particular, can calculate a p-value by a permutation test. Alignments of permuted sequences are calculated quickly using an aligner that only records the score (see SequenceAligner.alignFast()).

Example usage:

SequenceAligner<DnaSequence, NucleotideCompound> aligner =
	SequenceAligner.dna(Alignments.PairwiseSequenceAlignerType.GLOBAL)
	.setGapPenalty(new SimpleGapPenalty(11, 1))
	.setMatrix(SubstitutionMatrixHelper.getNuc4_4()) // the default anyway
	.build()
SequenceAlignmentWithPvalue<DnaSequence, NucleotideCompound> alignment
    = aligner.alignAndCalcPvalue(200, sequenceA, sequenceB);
    alignment.getPvalue(); // returns a double

Warning: there is currently a bug in the p-value calculations; see issue #1.

In addition, contiguous gaps are handled incorrectly; see Biojava issue #213.

The software is licensed under the Apache License, Version 2.0.