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.eval |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
|
pal.popgen |
Classes for providing 'classical' population genetics analyses.
|
pal.statistics |
Classes with useful for statistics (normal distribution,
Gamma distribution, chi-square distribution, exponential distribution,
likelihood-ratio test, chi-square test, descriptive statistics, bootstrap estimators etc.)
|
pal.tree |
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
|
pal.treesearch | |
pal.xml |
Utility classes for converting PAL objects to and from XML documents.
|
Modifier and Type | Interface | Description |
---|---|---|
interface |
AnnotationAlignment |
The AnnotationAlignment interface is designed to provide annotation for an alignment.
|
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 |
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 Alignment |
StrippedAlignment.rawAlignment |
Modifier and Type | Method | Description |
---|---|---|
static Alignment |
AlignmentUtils.concatAlignments(Alignment[] alignments,
DataType dt) |
Concatenates an array of alignments such that the resulting alignment is
all of the sub alignments place along side each other
|
static Alignment |
AlignmentTool.convertToUniversalAminoAcids(Alignment base,
int startingIndex) |
Convert an alignment to one of amino acids (using Universal Translation)
|
static Alignment |
AlignmentTool.createBootstrapReplicate(Alignment base) |
A simple approach to creating a bootstrap replicate
|
static Alignment |
AlignmentTool.createGapBalanced(Alignment base,
int startingIndex) |
Create a gap balanced alignment.
|
Alignment |
AlignmentBuilder.generateAlignment(DataType dt) |
Build an alignment based on sequences stored.
|
Alignment |
Genotype.getAlignment(int i) |
|
static Alignment |
AlignmentUtils.getChangedDataType(Alignment a,
DataType dt) |
Returns an alignment which follows the pattern of the input alignment
except that all sites which do not contain states in dt (excluding the
gap character) are removed.
|
Alignment |
AlignmentReceiver.SingleReceiver.getLastReceivedAlignment() |
|
static Alignment |
AlignmentUtils.getLeadingIncompleteCodonsStripped(Alignment base) |
Creates a new nucleotide alignment based on the input that has any leading incomplete
codons (that is, the first codon of the sequence that is not a gap/unknown but is not complete - has
a nucleotide unknown) replaced by a triplet of unknowns
|
Alignment |
AlignmentGenerator.getNextAlignment(AlgorithmCallback callback) |
|
Alignment[] |
AlignmentReceiver.BucketReceiver.getReceivedAlignments() |
|
static Alignment |
AlignmentTool.readAlignment(java.io.Reader r,
DataType dt) |
Attempt to read a file from a reader object
|
static Alignment[] |
AlignmentReaders.readAllPhylipClustalAlignments(java.io.Reader r,
DataType dt) |
Read an alignment in phylip/clustal/simple format.
|
static Alignment |
AlignmentReaders.readFastaSequences(java.io.Reader r,
DataType dt) |
Read an a set of unaligned Fasta sequences
|
static Alignment |
AlignmentReaders.readNewLineSeperatedSequences(java.io.Reader r,
DataType dt) |
Read an a set of unaligned Fasta sequences
|
static Alignment |
AlignmentReaders.readPhylipClustalAlignment(java.io.Reader r,
DataType dt) |
Read an alignment in phylip/clustal/simple format.
|
static Alignment |
AlignmentUtils.removeRedundantSites(Alignment a) |
|
Alignment |
DataTranslator.toAlignment(MolecularDataType dt,
int startingIndex) |
|
Alignment |
DataTranslator.toLeftAlignedReverseComplementNucleotides(int startingIndex) |
|
Alignment |
DataTranslator.toReverseComplementNucleotides(int startingIndex) |
Modifier and Type | Method | Description |
---|---|---|
static Alignment |
AlignmentUtils.concatAlignments(Alignment[] alignments,
DataType dt) |
Concatenates an array of alignments such that the resulting alignment is
all of the sub alignments place along side each other
|
static Alignment |
AlignmentTool.convertToUniversalAminoAcids(Alignment base,
int startingIndex) |
Convert an alignment to one of amino acids (using Universal Translation)
|
static int |
AlignmentUtils.countUnknowns(Alignment a,
DataType dt) |
Tests the characters of an alignment to see if there are any characters that
are not within a data type.
|
static AlignmentGenerator |
AlignmentGenerator.Utils.createBootstrapGenerator(Alignment baseAlignment) |
|
static Alignment |
AlignmentTool.createBootstrapReplicate(Alignment base) |
A simple approach to creating a bootstrap replicate
|
static Alignment |
AlignmentTool.createGapBalanced(Alignment base,
int startingIndex) |
Create a gap balanced alignment.
|
static double[] |
AlignmentUtils.estimateCodonFrequenciesF1X4(Alignment a) |
Estimate the frequencies of codons, calculated from the average nucleotide frequencies.
|
static double[] |
AlignmentUtils.estimateCodonFrequenciesF3X4(Alignment a) |
Estimate the frequencies of codons, calculated from the average nucleotide
frequencies at the three codon positions.
|
static double[] |
AlignmentUtils.estimateFrequencies(Alignment a) |
count states
|
static double[][] |
AlignmentUtils.estimateTupletFrequencies(Alignment a,
int tupletSize) |
Estimates frequencies via tuplets.
|
static void |
AlignmentUtils.getAlignedSequenceIndices(Alignment a,
int i,
int[] indices,
DataType dataType,
int unknownState) |
Returns state indices for a sequence.
|
static int[][] |
AlignmentUtils.getAlignedStates(Alignment base) |
Unknown characters are given the state of -1
|
static int[][] |
AlignmentUtils.getAlignedStates(Alignment base,
int unknownState) |
|
static double |
AlignmentUtils.getAlignmentPenalty(Alignment a,
DataType dataType,
TransitionPenaltyTable penalties,
double gapCreation,
double gapExtension,
boolean local) |
Returns total sum of pairs alignment distance using gap creation
and extension penalties and transition penalties as defined in the
TransitionPenaltyTable provided.
|
static double |
AlignmentUtils.getAlignmentPenalty(Alignment a,
TransitionPenaltyTable penalties,
double gapCreation,
double gapExtension) |
Returns total sum of pairs alignment penalty using gap creation
and extension penalties and transition penalties in the
TransitionPenaltyTable provided.
|
static Alignment |
AlignmentUtils.getChangedDataType(Alignment a,
DataType dt) |
Returns an alignment which follows the pattern of the input alignment
except that all sites which do not contain states in dt (excluding the
gap character) are removed.
|
static double |
AlignmentUtils.getConsistency(Alignment a,
Alignment b) |
|
static Alignment |
AlignmentUtils.getLeadingIncompleteCodonsStripped(Alignment base) |
Creates a new nucleotide alignment based on the input that has any leading incomplete
codons (that is, the first codon of the sequence that is not a gap/unknown but is not complete - has
a nucleotide unknown) replaced by a triplet of unknowns
|
static void |
AlignmentUtils.getPositionMisalignmentInfo(Alignment a,
java.io.PrintWriter out,
int startingCodonPosition) |
|
static void |
AlignmentUtils.getPositionMisalignmentInfo(Alignment a,
java.io.PrintWriter out,
int startingCodonPosition,
CodonTable translator,
boolean removeIncompleteCodons) |
|
static char[] |
AlignmentUtils.getSequenceCharArray(Alignment a,
int sequence) |
Returns a particular sequence of an alignment as a char array
|
static java.lang.String |
AlignmentUtils.getSequenceString(Alignment a,
int sequence) |
Returns a particular sequence of an alignment as a String
|
static SitePattern |
SitePattern.getSitePattern(Alignment a) |
|
static DataType |
AlignmentUtils.getSuitableInstance(Alignment alignment) |
guess data type suitable for a given sequence data set
|
static boolean |
AlignmentUtils.isGap(Alignment a,
int seq,
int site) |
Returns true if the alignment has a gap at the site in the
sequence specified.
|
static boolean |
AlignmentUtils.isSiteRedundant(Alignment a,
int site) |
|
void |
AlignmentReceiver.BucketReceiver.newAlignment(Alignment a) |
|
void |
AlignmentReceiver.newAlignment(Alignment a) |
|
void |
AlignmentReceiver.SingleReceiver.newAlignment(Alignment a) |
|
static void |
AlignmentUtils.print(Alignment a,
java.io.PrintWriter out) |
print alignment (default format: INTERLEAVED)
|
static void |
AlignmentUtils.printCLUSTALW(Alignment a,
java.io.PrintWriter out) |
Print alignment (in CLUSTAL W format)
|
static void |
AlignmentUtils.printInterleaved(Alignment a,
java.io.PrintWriter out) |
print alignment (in PHYLIP 3.4 INTERLEAVED format)
|
static void |
AlignmentUtils.printPlain(Alignment a,
java.io.PrintWriter out) |
print alignment (in plain format)
|
static void |
AlignmentUtils.printPlain(Alignment a,
java.io.PrintWriter out,
boolean relaxed) |
print alignment (in plain format)
|
static void |
AlignmentUtils.printSequential(Alignment a,
java.io.PrintWriter out) |
print alignment (in PHYLIP SEQUENTIAL format)
|
static Alignment |
AlignmentUtils.removeRedundantSites(Alignment a) |
|
static void |
AlignmentUtils.report(Alignment a,
java.io.PrintWriter out) |
Report number of sequences, sites, and data type
|
static int[][] |
DataTranslator.toStates(Alignment a) |
Converts an alignment to a state matrix
Stored as [sequnce][site]
|
static int[][] |
DataTranslator.toStates(Alignment a,
int gapUnknownState) |
Converts an alignment to a state matrix
Stored as [sequnce][site]
|
Constructor | Description |
---|---|
BootstrappedAlignment(Alignment raw) |
Constructor
|
ConcatenatedAlignment(Alignment[] list) |
concatenate alignments
|
DataTranslator(Alignment base) |
|
GapBalancedAlignment(Alignment base,
int startingCodonPosition,
boolean alignGap) |
The standard GapBalanced constructor
|
GapBalancedAlignment(Alignment base,
int startingCodonPosition,
boolean alignGap,
int codonLength) |
GapBalanced power user constructor
|
GapBalancedAlignment(Alignment base,
int startingCodonPosition,
int codonLength) |
GapBalanced power user constructor
|
Genotype(Alignment a1,
Alignment a2) |
|
IndelAlignment(Alignment a,
boolean anchored) |
Basic constructor.
|
JumbledAlignment(Alignment raw) |
|
MultiLocusAnnotatedAlignment(Alignment a) |
Basic constructor.
|
SimpleAlignment(Alignment a) |
Clone constructor.
|
SimpleAlignment(Alignment a,
int sequenceToIgnore) |
Clone constructor.
|
SimpleAlignment(Alignment a,
Alignment b,
java.lang.String guide1,
java.lang.String guide2,
char gap) |
This constructor combines to alignments given two guide strings.
|
SimpleAlignment(Alignment a,
LabelMapping lm) |
Clone constructor.
|
SimpleAnnotatedAlignment(Alignment a) |
Clone constructor from an unannotated alignment.
|
SitePattern(Alignment a) |
infer site patterns for a given alignment
|
StrippedAlignment(Alignment raw) |
Constructor
|
Modifier and Type | Method | Description |
---|---|---|
Alignment[] |
SerialCoalescentGenerator.Results.getAlignments() |
Constructor | Description |
---|---|
Results(Tree[] trees,
Alignment[] alignments) |
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.
|
static DistanceMatrixAccess |
DistanceMatrixAccess.Utils.createEvolutionary(Alignment a,
SubstitutionModel sm) |
|
static DistanceMatrixGenerator |
DistanceMatrixGenerator.Utils.createEvolutionary(Alignment a,
SubstitutionModel sm) |
Constructor | Description |
---|---|
JukesCantorDistanceMatrix(Alignment alignment) |
compute jukes-cantor corrected distances
|
Modifier and Type | Method | Description |
---|---|---|
static Alignment |
LikelihoodTool.getMatchingDataType(Alignment alignment,
SubstitutionModel model) |
Creates a new alignment that has a compatible data type with a substution model (needed for likelihood stuff)
|
Modifier and Type | Method | Description |
---|---|---|
static double |
LikelihoodTool.calculateLogLikelihood(Tree tree,
Alignment alignment,
SubstitutionModel model) |
Calculate the log likelihood of a particular set of phylogenetic data
|
static Alignment |
LikelihoodTool.getMatchingDataType(Alignment alignment,
SubstitutionModel model) |
Creates a new alignment that has a compatible data type with a substution model (needed for likelihood stuff)
|
static double |
LikelihoodOptimiser.optimiseAlternate(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits) |
Optimise parameters to acheive maximum likelihood using an alternating stategy.
|
static double |
LikelihoodOptimiser.optimiseAlternate(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor) |
Optimise parameters to acheive maximum likelihood using an alternating stategy.
|
static Tree |
LikelihoodTool.optimiseClockConstrained(Tree tree,
Alignment alignment,
SubstitutionModel model,
boolean optimiseModel) |
Optimise the branches of a tree with regard to maximum likelihood, with a molecular clock assumption, that is, constrained such that all tips are contemporaneous, the tree is treated as rooted.
|
static double |
LikelihoodOptimiser.optimiseCombined(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits) |
Optimise parameters to acheive maximum likelihood using a combined stategy.
|
static double |
LikelihoodOptimiser.optimiseCombined(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor) |
Optimise parameters to acheive maximum likelihood using a combined stategy.
|
static double |
LikelihoodOptimiser.optimiseModel(Tree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor) |
Optimise model parameters only to acheive maximum likelihood using a combined stategy.
|
static Tree |
LikelihoodTool.optimiseMRDT(Tree tree,
Alignment alignment,
SubstitutionModel model,
TimeOrderCharacterData tocd,
boolean optimiseModel,
double[] rateStore) |
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu - one for each sampling interval.
|
static Tree |
LikelihoodTool.optimiseMRDT(Tree tree,
Alignment alignment,
SubstitutionModel model,
TimeOrderCharacterData tocd,
boolean optimiseModel,
double[] rateChangeTimes,
double[] rateStore) |
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu, over general time intervals.
|
static Tree |
LikelihoodTool.optimiseSRDT(Tree tree,
Alignment alignment,
SubstitutionModel model,
TimeOrderCharacterData tocd,
boolean optimiseModel,
double[] rateStore) |
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and a single mutation rate parameter.
|
static double |
LikelihoodOptimiser.optimiseTree(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits) |
Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy.
|
static double |
LikelihoodOptimiser.optimiseTree(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor) |
Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy.
|
static Tree |
LikelihoodTool.optimiseUnrooted(Tree tree,
Alignment alignment,
SubstitutionModel model,
boolean optimiseModel) |
Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).
|
Constructor | Description |
---|---|
GeneralLikelihoodCalculator(Alignment baseAlignment,
Tree tree,
RateMatrix model) |
Constructor taking site pattern, tree and a rate matrix.
|
GeneralLikelihoodCalculator(Alignment baseAlignment,
Tree tree,
RateMatrix model,
RateDistribution distribution) |
Constructor taking site pattern, tree rate matrix, and a rate distribution
|
GeneralLikelihoodCalculator(Alignment baseAlignment,
Tree tree,
SubstitutionModel model) |
Constructor taking site pattern, tree and a general substitution model.
|
LikelihoodOptimiser(Tree tree,
Alignment alignment,
SubstitutionModel model) |
Modifier and Type | Field | Description |
---|---|---|
protected Alignment |
LinkageDisequilibrium.theAlignment |
Constructor | Description |
---|---|
LinkageDisequilibrium(Alignment alignment) |
compute LD based on an alignment.
|
LinkageDisequilibrium(Alignment alignment,
boolean rapidPermute,
int numberOfPermutations) |
compute LD based on an alignment
|
Modifier and Type | Method | Description |
---|---|---|
double |
LikelihoodEvaluator.calculateLikelihood(Tree tree,
Alignment alignment) |
|
LikelihoodEvaluator.MLResult |
LikelihoodEvaluator.getMLOptimised(Tree tree,
Alignment alignment,
AlgorithmCallback callback) |
|
double |
ReplicateLikelihoodEvaluator.getReplicateLogLikelihood(Tree tree,
Alignment alignment) |
Constructor | Description |
---|---|
GeneralTopologyPool(Tree[] topologies,
LikelihoodEvaluator baseCalculator,
ReplicateLikelihoodEvaluator replicateCalculator,
Alignment baseAlignment,
AlignmentGenerator replicateGenerator) |
Modifier and Type | Class | Description |
---|---|---|
class |
SimulatedAlignment |
generates an artificial data set
|
Modifier and Type | Method | Description |
---|---|---|
static Alignment |
TreeUtils.extractAlignment(Tree tree) |
Extracts an alignment from a tree.
|
static Alignment |
TreeUtils.extractAlignment(Tree tree,
boolean leaveSeqsInTree) |
Extracts an alignment from a tree.
|
Modifier and Type | Method | Description |
---|---|---|
static Alignment |
TreeSearchTool.getMatchingDataType(Alignment alignment,
SubstitutionModel model) |
Creates a new alignment that has a compatible data type with a substution model (needed for likelihood stuff)
|
Modifier and Type | Method | Description |
---|---|---|
UnrootedMLSearcher |
BranchAccess.attach(java.lang.String newSequence,
Alignment fullAlignment) |
Create a new Tree Searcher with a new sub tree attached
|
UnrootedMLSearcher |
BranchAccess.attach(java.lang.String newSequence,
Alignment fullAlignment,
SubstitutionModel model) |
Create a new Tree Searcher with a new sub tree attached
|
UnrootedMLSearcher |
BranchAccess.attach(Node subTree,
Alignment fullAlignment) |
Create a new Tree Searcher with a new sub tree attached
|
UnrootedMLSearcher |
BranchAccess.attach(Node subTree,
Alignment fullAlignment,
SubstitutionModel model) |
Create a new Tree Searcher with a new sub tree attached
|
Tree |
TreeSearchTool.basicUnrootedTreeMLSearch(Alignment a,
SubstitutionModel sm,
boolean optimiseModel) |
Do a basic tree search using maximum likelihood on an unrooted tree space, without a given starting tree
|
Tree |
TreeSearchTool.basicUnrootedTreeMLSearch(Alignment a,
SubstitutionModel sm,
boolean optimiseModel,
AlgorithmCallback callback) |
Do a basic tree search using maximum likelihood on an unrooted tree space, without a given starting tree
|
Tree |
TreeSearchTool.basicUnrootedTreeMLSearch(Tree baseTree,
Alignment a,
SubstitutionModel sm,
boolean optimiseModel) |
Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting tree
|
Tree |
TreeSearchTool.basicUnrootedTreeMLSearch(Tree baseTree,
Alignment a,
SubstitutionModel sm,
boolean optimiseModel,
AlgorithmCallback callback) |
Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting tree
|
static double |
TreeSearchTool.calculateLogLikelihood(Tree tree,
Alignment alignment,
SubstitutionModel model) |
Calculate the log likelihood of a particular set of phylogenetic data
|
static Alignment |
TreeSearchTool.getMatchingDataType(Alignment alignment,
SubstitutionModel model) |
Creates a new alignment that has a compatible data type with a substution model (needed for likelihood stuff)
|
static Tree |
TreeSearchTool.optimiseClockConstrainedFixed(Tree tree,
Alignment alignment,
SubstitutionModel model,
boolean optimiseModel,
AlgorithmCallback callback) |
Optimise the branches of a tree with regard to maximum likelihood, with the contraints of a global molecular clock - that is, all the tips terminate at the same point.
|
static Tree |
TreeSearchTool.optimiseUnrootedFixed(Tree tree,
Alignment alignment,
SubstitutionModel model,
boolean optimiseModel) |
Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).
|
static Tree |
TreeSearchTool.optimiseUnrootedFixed(Tree tree,
Alignment alignment,
SubstitutionModel model,
boolean optimiseModel,
AlgorithmCallback callback) |
Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).
|
Constructor | Description |
---|---|
GeneralConstructionTool(ConstraintModel constraints,
Alignment alignment) |
The constructor
|
GeneralLikelihoodSearcher(Node baseTopology,
Alignment baseAlignment,
ConstraintModel constraintModel) |
|
UnrootedMLSearcher(Alignment alignment,
SubstitutionModel model) |
Build an unconstrained optimiser based on a randomly generated tree.
|
UnrootedMLSearcher(Alignment alignment,
SubstitutionModel model,
LHCalculator.Factory calcFactory) |
|
UnrootedMLSearcher(Node root,
Alignment alignment,
SubstitutionModel model) |
|
UnrootedMLSearcher(Node root,
Alignment alignment,
SubstitutionModel model,
LHCalculator.Factory calcFactory) |
|
UnrootedMLSearcher(Tree t,
Alignment alignment,
SubstitutionModel model) |
Modifier and Type | Method | Description |
---|---|---|
static Alignment |
ElementParser.parseAlignmentElement(org.w3c.dom.Element e) |
Parses an alignment element and returns an alignment object.
|
Modifier and Type | Method | Description |
---|---|---|
static org.w3c.dom.Element |
ElementFactory.createAlignmentElement(Alignment a,
org.w3c.dom.Document document) |
|
protected static RateMatrix |
ElementParser.parseRateMatrix(org.w3c.dom.Element e,
Alignment a) |
Reads a rate matrix from a DOM Document element.
|