Package | Description |
---|---|
jebl.evolution.align |
Provides classes and interfaces for pairwise alignment of two sequences.
|
jebl.evolution.trees |
Modifier and Type | Method and Description |
---|---|
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) |
Modifier and Type | Method and Description |
---|---|
static TreeBuilderFactory.Method |
TreeBuilderFactory.Method.valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.
|
static TreeBuilderFactory.Method[] |
TreeBuilderFactory.Method.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Modifier and Type | Method and Description |
---|---|
static ClusteringTreeBuilder |
TreeBuilderFactory.getBuilder(TreeBuilderFactory.Method method,
DistanceMatrix distances) |
static ClusteringTreeBuilder |
ClusteringTreeBuilder.getBuilder(TreeBuilderFactory.Method method,
DistanceMatrix distances)
A factory method to create a ClusteringTreeBuilder
|
static boolean |
TreeBuilderFactory.isRootedMethod(TreeBuilderFactory.Method method) |
http://code.google.com/p/jebl2/