Package | Description |
---|---|
pal.distance |
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
|
pal.eval |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
|
pal.supgma | |
pal.tree |
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
|
Modifier and Type | Class | Description |
---|---|---|
class |
AlignmentDistanceMatrix |
compute distance matrix (observed and ML) from alignment (SitePattern)
|
class |
JukesCantorDistanceMatrix |
compute jukes-cantor corrected distance matrix
|
class |
ReadDistanceMatrix |
reads pairwise distance matrices in PHYLIP format
(full matrix)
|
Modifier and Type | Method | Description |
---|---|---|
static DistanceMatrix |
DistanceTool.constructEvolutionaryDistances(Alignment a,
SubstitutionModel sm) |
Construct a distance matrix object such that the distance between sequence A, and sequence B, is the
evolutionary distance by a given substitution model.
|
DistanceMatrix |
DistanceMatrixGenerator.generateNextMatrix(AlgorithmCallback callback) |
|
static DistanceMatrix |
DistanceMatrixUtils.minus(DistanceMatrix parent,
int taxaToRemove) |
Returns a distance matrix with the specified taxa removed.
|
DistanceMatrix |
DistanceMatrixAccess.obtainMatrix(AlgorithmCallback callback) |
Modifier and Type | Method | Description |
---|---|---|
double |
DistanceMatrix.absoluteDistance(DistanceMatrix mat) |
compute absolute distance to second distance matrix
|
static DistanceMatrixAccess |
DistanceMatrixAccess.Utils.createSimple(DistanceMatrix base) |
|
static DistanceMatrix |
DistanceMatrixUtils.minus(DistanceMatrix parent,
int taxaToRemove) |
Returns a distance matrix with the specified taxa removed.
|
double |
DistanceMatrix.squaredDistance(DistanceMatrix mat,
boolean weighted) |
compute squared distance to second distance matrix
|
static double |
DistanceMatrixUtils.squaredDistance(DistanceMatrix mat1,
DistanceMatrix mat2,
boolean weighted) |
compute squared distance to second distance matrix.
|
Constructor | Description |
---|---|
DistanceMatrix(DistanceMatrix dm) |
constructor that takes a distance matrix and clones the distances
but uses the same idGroup.
|
DistanceMatrix(DistanceMatrix dm,
IdGroup subset) |
constructor that takes a distance matrix and clones the distances,
of a the identifiers in idGroup.
|
JukesCantorDistanceMatrix(DistanceMatrix dist) |
compute jukes-cantor corrected distances
(assumes nucleotides as underlying data)
|
JukesCantorDistanceMatrix(DistanceMatrix dist,
int numStates) |
compute jukes-cantor corrected distances
|
Constructor | Description |
---|---|
ChiSquareValue(DistanceMatrix m,
boolean w) |
initialization
|
Modifier and Type | Class | Description |
---|---|---|
class |
SUPGMADistanceMatrix |
Corrects distances in a distance matrix such that all tips appear
contemporaneous, given a time/date and rate information for the
taxa.
|
Constructor | Description |
---|---|
SUPGMADistanceMatrix(DistanceMatrix raw,
TimeOrderCharacterData tocd,
DeltaModel deltaModel) |
Uses date/time information and a constant rate to correct distance matrices.
|
SUPGMATree(DistanceMatrix m,
TimeOrderCharacterData tocd,
double rate,
ClusterTree.ClusteringMethod cm) |
constructor SUPGMA tree
|
SUPGMATree(DistanceMatrix m,
TimeOrderCharacterData tocd,
DeltaModel deltaModel,
boolean allowNegatives,
ClusterTree.ClusteringMethod cm) |
constructor SUPGMA tree
|
Modifier and Type | Class | Description |
---|---|---|
class |
TreeDistanceMatrix |
computes distance matrix induced by a tree
(needs only O(n^2) time, following algorithm DistanceInTree by
D.Bryant and P.
|
Modifier and Type | Method | Description |
---|---|---|
static Tree |
TreeTool.createNeighbourJoiningTree(DistanceMatrix dm) |
Neighbour-joining tree construction based on a distance matrix
|
static Tree |
TreeTool.createUPGMA(DistanceMatrix dm) |
UPGMA tree construction based on a distance matrix
|
Constructor | Description |
---|---|
ClusterTree(DistanceMatrix dm,
ClusterTree.ClusteringMethod cm) |
|
NeighborJoiningTree(DistanceMatrix m) |
construct NJ tree
|
UPGMATree(DistanceMatrix m) |
Deprecated.
constructor UPGMA tree
|