Package com.hfg.bio.seq.alignment

Class Summary

Class	Description
AlignedQuery	Container for the aligned query sequence part of a pairwise sequence alignment.
AlignedSeq	Base class for the aligned sequences that compose a pairwise sequence alignment.
AlignedSubject	Container for the aligned subject sequence part of a pairwise sequence alignment.
AlignmentScoring	Pairwise sequence alignment scoring data.
GapPenalties	Container for pairwise sequence alignment gap penalties.
KMerBitSet	BitSet container for holding detected k-mer instances from a sequence.
KMerSimilarity	A basic similarity assessment that uses k-mer analysis.
MSA_Settings	Container for multiple sequence alignment settings.
MultipleSequenceAligner<T extends BioSequence>	A basic multiple sequence aligner that uses an initial 3-mer analysis to produce a draft guide tree and then performs progressive pairwise alignments.
MultipleSequenceAlignment<T extends BioSequence>	Container for aligned sequences.
PairwiseSeqAligner	Tool for creating pairwise sequence alignments.
PairwiseSeqAlignment	Pairwise sequence alignment container.
PairwiseSettings	Container for pairwise sequence alignment settings.
PctId	Container for holding percent identity components.

Enum Summary

Enum	Description
PairwiseAlignmentType
PairwiseSeqTerminus	Created by taylora on 9/14/14.
PairwiseSeqType	Created by taylora on 9/14/14.