Package org.nmdp.ngs.align

Sequence alignment.

See: Description

Interface Summary

Interface	Description
BedListener	BED listener.
HspListener	High-scoring segment pair (HSP) listener.
PairwiseAlignment	Pairwise DNA sequence alignment.

Class Summary

Class	Description
Alignments	Static utility methods on alignments.
BedReader	BED format reader.
BedRecord	BED record.
BedWriter	BED writer.
BiojavaPairwiseAlignment	Serial implementation of PairwiseAlignment based on Biojava.
Blastn	Utility to run blastn via the command line.
GapPenalties	Gap penalties.
GapPenalties.Builder	Gap penalties builder.
Genewise	Utility to run genewise via the command line.
GenewiseExon	Genewise exon.
HighScoringPair	High-scoring segment pair (HSP).
HspReader	High-scoring segment pair (HSP) reader.
HspWriter	High-scoring segment pair (HSP) writer.
ParallelBiojavaPairwiseAlignment	Parallel implementation of PairwiseAlignment based on Biojava.

Package org.nmdp.ngs.align Description

Sequence alignment.