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 and 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 and Description |
---|---|
DistanceMatrix |
AlignmentTreeBuilderFactory.Result.distance |
Modifier and Type | Class and 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 and Description |
---|---|
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).
|
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).
|
Modifier and Type | Method and Description |
---|---|
DistanceMatrix |
NexusImporter.parseDistancesBlock(java.util.List<Taxon> taxonList)
Parse the next 'DISTANCES' block encountered in the input.
|
Modifier and Type | Method and 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 and Description |
---|---|
void |
NexusExporter.exportMatrix(DistanceMatrix distanceMatrix) |
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
|
Constructor and Description |
---|
NeighborJoiningTreeBuilder(DistanceMatrix distanceMatrix)
construct NJ tree
|
http://code.google.com/p/jebl2/