Package | Description |
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jebl.evolution.align |
Provides classes and interfaces for pairwise alignment of two sequences.
|
jebl.evolution.distances |
Modifier and Type | Method and Description |
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java.lang.String[] |
BartonSternberg.align(java.util.List<Sequence> sourceSequences,
ProgressListener progress,
boolean refineOnly,
boolean estimateMatchMismatchCosts) |
static AlignmentTreeBuilderFactory.Result |
AlignmentTreeBuilderFactory.build(Alignment alignment,
TreeBuilderFactory.Method method,
TreeBuilderFactory.DistanceModel model,
ProgressListener progressListener) |
static AlignmentTreeBuilderFactory.Result |
AlignmentTreeBuilderFactory.build(Alignment alignment,
TreeBuilderFactory.Method method,
TreeBuilderFactory.DistanceModel model,
ProgressListener progressListener,
boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable) |
static AlignmentTreeBuilderFactory.Result |
AlignmentTreeBuilderFactory.build(java.util.List<Sequence> seqs,
TreeBuilderFactory.Method method,
MultipleAligner aligner,
ProgressListener progress,
boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable) |
static AlignmentTreeBuilderFactory.Result |
AlignmentTreeBuilderFactory.build(java.util.List<Sequence> seqs,
TreeBuilderFactory.Method method,
PairwiseAligner aligner,
ProgressListener progressListener)
Will use model F84 for nucleotides and Jukes-Cantor for amino acid
|
static AlignmentTreeBuilderFactory.Result |
AlignmentTreeBuilderFactory.build(java.util.List<Sequence> seqs,
TreeBuilderFactory.Method method,
PairwiseAligner aligner,
ProgressListener progressListener,
TreeBuilderFactory.DistanceModel model) |
Constructor and Description |
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SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs,
PairwiseAligner aligner,
ProgressListener progress) |
SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs,
PairwiseAligner aligner,
ProgressListener progress,
TreeBuilderFactory.DistanceModel model) |
Constructor and Description |
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HKYDistanceMatrix(Alignment alignment,
ProgressListener progress) |
HKYDistanceMatrix(Alignment alignment,
ProgressListener progress,
boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable) |
JukesCantorDistanceMatrix(Alignment alignment,
ProgressListener progress) |
JukesCantorDistanceMatrix(Alignment alignment,
ProgressListener progress,
boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable) |
TamuraNeiDistanceMatrix(Alignment alignment,
ProgressListener progress) |
TamuraNeiDistanceMatrix(Alignment alignment,
ProgressListener progress,
boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable) |
http://code.google.com/p/jebl2/