See: Description
Interface | Description |
---|---|
MultipleAligner | |
PairwiseAligner | |
TracebackPlotter |
Class | Description |
---|---|
Align | |
AlignCommand |
A command line interface for the algorithms in jebl.evolution.align.
|
AlignmentTreeBuilderFactory | |
AlignmentTreeBuilderFactory.Result | |
BartonSternberg | |
MaximalSegmentPair | |
NeedlemanWunsch | |
NeedlemanWunschAffine | |
NeedlemanWunschLinearSpace | |
NeedlemanWunschLinearSpaceAffine | |
NonOverlapMultipleLocalAffine |
Performs recursive local alignments.
|
OldNeedlemanWunschAffine | |
Output | |
OverlapAlign | |
PairwiseAligner.Result | |
ProfileCharacter | |
SequenceAlignmentsDistanceMatrix |
Builds a distance matrix by performing a series of pairwise alignments between the
specified sequences (unlike the methods in jebl.evolution.distances, which
extract the pairwise distances from a multiple sequence alignment).
|
SequenceShuffler |
Shuffles a sequence and aligns it again multiple times to give mean and variance of
alignments on random sequences.
|
SmithWaterman | |
SmithWatermanLinearSpace | |
SmithWatermanLinearSpaceAffine | |
SystemOut | |
Traceback |
Some of the classes in this package are based on source code by Peter Sestoft, sestoft@dina.kvl.dk. His original source code can be at http://www.dina.kvl.dk/~sestoft/bsa.html
http://code.google.com/p/jebl2/