Package | Description |
---|---|
pal.alignment |
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
|
pal.coalescent |
Classes to model population genetic processes using the coalescent.
|
pal.distance |
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
|
pal.misc |
Classes that don't fit elsewhere ;^)
|
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 | Interface | Description |
---|---|---|
interface |
Alignment |
interface for any alignment data.
|
interface |
AnnotationAlignment |
The AnnotationAlignment interface is designed to provide annotation for an alignment.
|
interface |
CharacterAlignment |
This interface is designed to hold quantitative character states.
|
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractAlignment |
abstract base class for any alignment data.
|
static class |
AlignmentReaders.PhylipClustalAlignment |
|
static class |
AlignmentReaders.UnalignedAlignment |
|
class |
BootstrappedAlignment |
generates bootstrapped alignments from a raw alignment
|
class |
ConcatenatedAlignment |
concatenates a list of alignments to one single alignment,
increasing the number of sites
|
class |
ConcatenatedAnnotatedAlignment |
This is an annotation version of the ConcatenatedAlignment
Unlike normal ConcatenatedAlignment, it permits for merges with different numbers
of sequences.
|
class |
GapBalancedAlignment |
Creates a "Gap-Balanced" alignment.
|
class |
IndelAlignment |
This class extracts indels (insertion/deletion) out of an alignment, and creates
an alignment of indel polymorphisms.
|
class |
IndelAnnotatedAlignment |
an extension of the IndelAlignment that includes annotation.
|
class |
JumbledAlignment |
generates jumbled alignments (randomizing input order of sequences)
|
class |
MultiLocusAnnotatedAlignment |
MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple
loci.
|
class |
ReadAlignment |
reads aligned sequence data from plain text files.
|
class |
ReadAlignmentOld |
reads aligned sequence data from plain text files.
|
class |
SimpleAlignment |
An alignment class that can be efficiently constructed
from an array of strings.
|
class |
SimpleAnnotatedAlignment |
This is the basic implementation of the Annotation interface, which is designed to
provide annotation for an alignment.
|
class |
SimpleCharacterAlignment |
This provides a basic implementation of CharacterAlignment.
|
class |
SitePattern |
takes an Alignment and determines its site patterns
|
class |
StrippedAlignment |
takes an alignment and repeatedly removes sites
|
class |
StrippedAnnotatedAlignment |
This is the stripped implementation of the Annotation interface, which is designed to
provide stripped and annotated alignments.
|
Modifier and Type | Field | Description |
---|---|---|
protected IdGroup |
AbstractAlignment.idGroup |
sequence identifiers
|
protected IdGroup |
SimpleCharacterAlignment.idGroup |
sequence identifiers
|
Modifier and Type | Method | Description |
---|---|---|
protected void |
MultiLocusAnnotatedAlignment.init(IdGroup group,
java.lang.String[] sequences) |
Constructor | Description |
---|---|
DataTranslator(int[][] stateData,
MolecularDataType dt,
IdGroup ids) |
|
MultiLocusAnnotatedAlignment(AnnotationAlignment a,
IdGroup newGroup) |
This constructor will subset the alignment based on the taxa in IdGroup
|
MultiLocusAnnotatedAlignment(IdGroup group,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt) |
|
MultiLocusAnnotatedAlignment(IdGroup group,
java.lang.String[] sequences,
DataType dt) |
|
SimpleAlignment(IdGroup group,
char[][] cSequences,
java.lang.String gaps,
DataType dt) |
|
SimpleAlignment(IdGroup group,
char[][] cSequences,
DataType dt) |
|
SimpleAlignment(IdGroup ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt) |
|
SimpleAlignment(IdGroup ids,
java.lang.String[] sequences,
DataType dt) |
|
SimpleAlignment(IdGroup group,
DataType dt,
int[][] sSequences) |
|
SimpleAnnotatedAlignment(AnnotationAlignment a,
IdGroup newGroup) |
This constructor will subset the alignment based on the taxa in IdGroup
|
SimpleAnnotatedAlignment(IdGroup group,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt) |
This constructor creates a basic SimpleAnnotatedAlignment.
|
SimpleAnnotatedAlignment(IdGroup group,
java.lang.String[] sequences,
DataType dt) |
This constructor creates a basic SimpleAnnotatedAlignment.
|
SimpleCharacterAlignment(IdGroup group,
double[][] traitValues,
java.lang.String[] traitNames) |
Constructor for SimpleCharacterAlignment.
|
SimpleCharacterAlignment(IdGroup group,
double[][] traitValues,
java.lang.String[] traitNames,
java.lang.String[] environNames) |
Constructor for SimpleCharacterAlignment
|
SimpleCharacterAlignment(IdGroup group,
double[] traitValue,
java.lang.String traitName) |
Constructor for SimpleCharacterAlignment when there is only a single trait.
|
SitePattern(DataType dataType,
int numSites,
int numSeqs,
IdGroup idGroup,
int numPatterns,
int[] alias,
int[] weight,
byte[][] pattern) |
construct SitePattern from scratch
|
Modifier and Type | Class | Description |
---|---|---|
class |
DemographicClockTree |
Provides parameter interface to a clock-like genealogy which is
assumed to have some demographic pattern of theta (diversity) as
well as branch parameters (the minimal node height differences
at each internal node).
|
Modifier and Type | Class | Description |
---|---|---|
class |
AlignmentDistanceMatrix |
compute distance matrix (observed and ML) from alignment (SitePattern)
|
class |
DistanceMatrix |
storage for pairwise distance matrices.
|
class |
JukesCantorDistanceMatrix |
compute jukes-cantor corrected distance matrix
|
class |
ReadDistanceMatrix |
reads pairwise distance matrices in PHYLIP format
(full matrix)
|
Modifier and Type | Method | Description |
---|---|---|
IdGroup |
DistanceMatrix.getIdGroup() |
Deprecated.
distance matrix now implements IdGroup
|
Modifier and Type | Method | Description |
---|---|---|
protected void |
DistanceMatrix.setIdGroup(IdGroup base) |
Constructor | Description |
---|---|
DistanceMatrix(double[][] distance,
IdGroup idGroup) |
constructor taking distances array and IdGroup
|
DistanceMatrix(DistanceMatrix dm,
IdGroup subset) |
constructor that takes a distance matrix and clones the distances,
of a the identifiers in idGroup.
|
Modifier and Type | Class | Description |
---|---|---|
class |
SimpleIdGroup |
Default implementation of IdGroup interface.
|
class |
TimeOrderCharacterData |
Character data that expresses an order through time.
|
Modifier and Type | Field | Description |
---|---|---|
protected IdGroup |
TimeOrderCharacterData.taxa |
the identifier group
|
Modifier and Type | Method | Description |
---|---|---|
static IdGroup |
IdGenerator.createIdGroup(int size) |
generates a group of unique identifiers numbered from zero.
|
IdGroup |
TimeOrderCharacterData.getIdGroup() |
Deprecated.
TimeOrderCharacterData now implements IdGroup
|
IdGroup |
LabelMapping.getMapped(IdGroup original) |
Modifier and Type | Method | Description |
---|---|---|
static Identifier[] |
Identifier.getIdentifiers(IdGroup idGroup) |
Translates an IdGroup into an array of identifiers
|
IdGroup |
LabelMapping.getMapped(IdGroup original) |
|
static java.lang.String[] |
Identifier.getNames(IdGroup ids) |
Translates an IdGroup into an array of strings
|
static java.lang.String[] |
Identifier.getNames(IdGroup ids,
int toIgnore) |
Translates an IDgroup into an array of strings, with optional removal of particular identifier
|
static java.lang.String[] |
Identifier.getNames(IdGroup ids,
int[] toIgnore) |
Translates an IDgroup into an array of strings, with optional removal of particular identifier
|
TimeOrderCharacterData |
TimeOrderCharacterData.getReordered(IdGroup base) |
Creates a new TimeOrderCharacterData object with the same properites as this one
but the identifier positions match that of base (ie whichIdNumber(Name) returns the same as for base)
|
static boolean |
IdGroup.Utils.isContainedWithin(IdGroup sub,
IdGroup full) |
|
static boolean |
IdGroup.Utils.isEqualIgnoringOrder(IdGroup id1,
IdGroup id2) |
|
void |
TimeOrderCharacterData.setOrdinals(TimeOrderCharacterData tocd,
IdGroup standard,
boolean doTimes) |
Set time ordinals from another TimeOrderCharacterData.
|
TimeOrderCharacterData |
TimeOrderCharacterData.subset(IdGroup staxa) |
Extracts a subset of a TimeOrderCharacterData.
|
static int |
IdGroup.Utils.whichIdNumber(IdGroup group,
java.lang.String s) |
A convenience implementation of whichIdNumber that can be used by
IdGroup implementations
|
Constructor | Description |
---|---|
SimpleIdGroup(IdGroup a) |
Impersonating Constructor.
|
SimpleIdGroup(IdGroup a,
int toIgnore) |
Impersonating Constructor.
|
SimpleIdGroup(IdGroup a,
IdGroup b) |
Constructor taking two separate id groups and merging them.
|
TimeOrderCharacterData(IdGroup taxa,
int units) |
Constructor taking only IdGroup.
|
TimeOrderCharacterData(IdGroup taxa,
int units,
boolean contemp) |
Constructor taking only IdGroup.
|
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.
|
class |
SUPGMATree |
constructs an SUPGMA tree from pairwise distances.
|
Modifier and Type | Interface | Description |
---|---|---|
interface |
ParameterizedTree |
abstract base class for a tree with an Parameterized interface
|
interface |
Tree |
Interface for a phylogenetic or genealogical tree.
|
Modifier and Type | Class | Description |
---|---|---|
class |
ClockTree |
provides parameter interface to a clock tree
(parameters are the minimal node height differences
at each internal node)
|
class |
ClusterTree |
|
class |
LogParameterizedTree |
This class logarithmically transforms tree parameters.
|
class |
MutationRateModelTree |
Provides parameter interface to any clock-like tree with
serially sampled tips (parameters are the minimal node height differences
at each internal node).
|
class |
NeighborJoiningTree |
constructs a neighbor-joining tree from pairwise distances
Saitou, N., and Nei, M., (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. |
static class |
ParameterizedTree.ParameterizedTreeBase |
For parameterisations that work by adjusting a base tree (that is, they aren't really
tree's themselves...)
|
class |
ReadTree |
constructs a tree reading in a New Hampshire treefile, taking care
for internal labels and branch lengths and binary/nonbinary and
rooted/unrooted trees
|
class |
SimpleTree |
data structure for a binary/non-binary rooted/unrooted trees
|
class |
SimulatedAlignment |
generates an artificial data set
|
static class |
Tree.TreeBase |
|
class |
TreeDistanceMatrix |
computes distance matrix induced by a tree
(needs only O(n^2) time, following algorithm DistanceInTree by
D.Bryant and P.
|
class |
UnconstrainedTree |
provides parameter interface to an unconstrained tree
(parameters are all available branch lengths)
|
class |
UPGMATree |
Deprecated.
Use ClusterTree
|
Modifier and Type | Method | Description |
---|---|---|
IdGroup |
CladeSystem.getIdGroup() |
get idGroup
|
IdGroup |
SplitSystem.getIdGroup() |
get idGroup
|
static IdGroup |
TreeUtils.getLeafIdGroup(Tree tree) |
get list of the identifiers of the external nodes
|
Modifier and Type | Method | Description |
---|---|---|
static void |
CladeSystem.getClade(IdGroup idGroup,
Node internalNode,
boolean[] clade) |
get clade for internal node
|
static CladeSystem |
CladeSystem.getClades(IdGroup idGroup,
Tree tree) |
creates a clade system from a tree
(using a pre-specified order of sequences)
|
static Tree |
TreeUtils.getNumberRelabelledTree(Tree baseTree,
IdGroup ids) |
Create a new tree such that the labels are redifined from a base tree in such a manner:
For each leaf label
If the base label is not a number the new label is just the original label
If the base label is a number the new label appropriately index label from a set identifiers
|
static void |
SplitUtils.getSplit(IdGroup idGroup,
Node internalNode,
boolean[] split) |
get split for branch associated with internal node
|
static SplitSystem |
SplitUtils.getSplits(IdGroup idGroup,
Tree tree) |
creates a split system from a tree
(using a pre-specified order of sequences)
|
static int[] |
TreeUtils.mapExternalIdentifiers(IdGroup idGroup,
Tree tree) |
map external identifiers in the tree to a set of given identifiers
(which can be larger than the set of external identifiers but
must contain all of them)
NOTE: for efficiency it is assumed that the node lists of the tree are
correctly maintained.
|
Constructor | Description |
---|---|
CladeSystem(IdGroup idGroup,
int size) |
|
SplitSystem(IdGroup idGroup,
int size) |
|
TreeDistanceMatrix(Tree t,
IdGroup idGroup) |
compute induced distance matrix using actual branch lengths
|
TreeDistanceMatrix(Tree t,
IdGroup idGroup,
boolean countEdges,
double epsilon) |
compute induced distance matrix
|