Package | Description |
---|---|
jebl.evolution.align |
Provides classes and interfaces for pairwise alignment of two sequences.
|
jebl.evolution.distances | |
jebl.evolution.io | |
jebl.evolution.trees |
Modifier and Type | Class | Description |
---|---|---|
class |
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).
|
Modifier and Type | Field | Description |
---|---|---|
DistanceMatrix |
AlignmentTreeBuilderFactory.Result.distance |
Modifier and Type | Class | Description |
---|---|---|
class |
BasicDistanceMatrix |
|
class |
F84DistanceMatrix |
|
class |
HKYDistanceMatrix |
Compute HKY corrected distance matrix
|
class |
JukesCantorDistanceMatrix |
Compute jukes-cantor corrected distance matrix for a set of aligned sequences.
|
class |
TamuraNeiDistanceMatrix |
Date: 22/01/2006
Time: 17:28:59
|
Modifier and Type | Method | Description |
---|---|---|
DistanceMatrix |
BasicDistanceMatrix.getSubmatrix(java.util.Collection<Taxon> taxonSubset) |
Gets a sub-matrix for only those taxa in the collection (all
of which should be present in this matrix).
|
DistanceMatrix |
DistanceMatrix.getSubmatrix(java.util.Collection<Taxon> taxa) |
Gets a sub-matrix for only those taxa in the collection (all
of which should be present in this matrix).
|
Modifier and Type | Method | Description |
---|---|---|
DistanceMatrix |
NexusImporter.parseDistancesBlock(java.util.List<Taxon> taxonList) |
Parse the next 'DISTANCES' block encountered in the input.
|
Modifier and Type | Method | Description |
---|---|---|
java.util.List<DistanceMatrix> |
DistanceMatrixImporter.importDistanceMatrices() |
importDistances.
|
java.util.List<DistanceMatrix> |
NexusImporter.importDistanceMatrices() |
Import all distance matrices from all DISTANCES blocks in the input form the current position.
|
java.util.List<DistanceMatrix> |
TabDelimitedImporter.importDistanceMatrices() |
importDistances.
|
Modifier and Type | Method | Description |
---|---|---|
void |
NexusExporter.exportMatrix(DistanceMatrix distanceMatrix) |
Modifier and Type | Method | Description |
---|---|---|
static ClusteringTreeBuilder |
ClusteringTreeBuilder.getBuilder(TreeBuilderFactory.Method method,
DistanceMatrix distances) |
A factory method to create a ClusteringTreeBuilder
|
static ClusteringTreeBuilder |
TreeBuilderFactory.getBuilder(TreeBuilderFactory.Method method,
DistanceMatrix distances) |
Constructor | Description |
---|---|
NeighborJoiningTreeBuilder(DistanceMatrix distanceMatrix) |
construct NJ tree
|
http://code.google.com/p/jebl2/