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