Uses of Package
com.hfg.bio.seq.alignment

Packages that use com.hfg.bio.seq.alignment

Package	Description
com.hfg.bio.seq
com.hfg.bio.seq.alignment
com.hfg.bio.seq.alignment.matrix

Classes in com.hfg.bio.seq.alignment used by com.hfg.bio.seq

Class and Description
MultipleSequenceAlignment Container for aligned sequences.

Classes in com.hfg.bio.seq.alignment used by com.hfg.bio.seq.alignment

Class and 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.
MSA_Settings Container for multiple sequence alignment settings.
MultipleSequenceAligner 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 Container for aligned sequences.
PairwiseAlignmentType
PairwiseSeqAligner Tool for creating pairwise sequence alignments.
PairwiseSeqAlignment Pairwise sequence alignment container.
PairwiseSeqTerminus Created by taylora on 9/14/14.
PairwiseSeqType Created by taylora on 9/14/14.
PairwiseSettings Container for pairwise sequence alignment settings.
PctId Container for holding percent identity components.

Classes in com.hfg.bio.seq.alignment used by com.hfg.bio.seq.alignment.matrix

Class and Description
MultipleSequenceAlignment Container for aligned sequences.