Uses of Interface pal.alignment.Alignment

Packages that use Alignment
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.

Uses of Alignment in pal.alignment

Subinterfaces of Alignment in pal.alignment
Modifier and Type	Interface	Description
`interface`	`AnnotationAlignment`	The AnnotationAlignment interface is designed to provide annotation for an alignment.

Classes in pal.alignment that implement 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.

Fields in pal.alignment declared as Alignment
Modifier and Type	Field	Description
`protected Alignment`	StrippedAlignment.`rawAlignment`

Methods in pal.alignment that return Alignment
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)`

Methods in pal.alignment with parameters of type Alignment
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]

Constructors in pal.alignment with parameters of type Alignment
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

Uses of Alignment in pal.coalescent

Methods in pal.coalescent that return Alignment
Modifier and Type Method Description

Alignment[] SerialCoalescentGenerator.Results.getAlignments()

Constructors in pal.coalescent with parameters of type Alignment
Constructor Description

Results(Tree[] trees, Alignment[] alignments)

Methods in pal.coalescent that return Alignment
Modifier and Type	Method	Description
`Alignment[]`	SerialCoalescentGenerator.Results.`getAlignments()`

Constructors in pal.coalescent with parameters of type Alignment
Constructor	Description
`Results(Tree[] trees, Alignment[] alignments)`

Uses of Alignment in pal.distance

Methods in pal.distance with parameters of type Alignment
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)`

Constructors in pal.distance with parameters of type Alignment
Constructor	Description
`JukesCantorDistanceMatrix(Alignment alignment)`	compute jukes-cantor corrected distances

Uses of Alignment in pal.eval

Methods in pal.eval that return Alignment
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)

Methods in pal.eval with parameters of type Alignment
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).

Constructors in pal.eval with parameters of type Alignment
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)`

Uses of Alignment in pal.popgen

Fields in pal.popgen declared as Alignment
Modifier and Type	Field	Description
`protected Alignment`	LinkageDisequilibrium.`theAlignment`

Constructors in pal.popgen with parameters of type Alignment
Constructor	Description
`LinkageDisequilibrium(Alignment alignment)`	compute LD based on an alignment.
`LinkageDisequilibrium(Alignment alignment, boolean rapidPermute, int numberOfPermutations)`	compute LD based on an alignment

Uses of Alignment in pal.statistics

Methods in pal.statistics with parameters of type 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)`

Constructors in pal.statistics with parameters of type Alignment
Constructor	Description
`GeneralTopologyPool(Tree[] topologies, LikelihoodEvaluator baseCalculator, ReplicateLikelihoodEvaluator replicateCalculator, Alignment baseAlignment, AlignmentGenerator replicateGenerator)`

Uses of Alignment in pal.tree

Classes in pal.tree that implement Alignment
Modifier and Type	Class	Description
`class`	`SimulatedAlignment`	generates an artificial data set

Methods in pal.tree that return Alignment
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.

Uses of Alignment in pal.treesearch

Methods in pal.treesearch that return Alignment
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)

Methods in pal.treesearch with parameters of type Alignment
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).

Constructors in pal.treesearch with parameters of type Alignment
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)`

Uses of Alignment in pal.xml

Methods in pal.xml that return Alignment
Modifier and Type	Method	Description
`static Alignment`	ElementParser.`parseAlignmentElement(org.w3c.dom.Element e)`	Parses an alignment element and returns an alignment object.

Methods in pal.xml with parameters of type Alignment
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.

Uses of Interfacepal.alignment.Alignment

Uses of Alignment in pal.alignment

Uses of Alignment in pal.coalescent

Uses of Alignment in pal.distance

Uses of Alignment in pal.eval

Uses of Alignment in pal.popgen

Uses of Alignment in pal.statistics

Uses of Alignment in pal.tree

Uses of Alignment in pal.treesearch

Uses of Alignment in pal.xml

Uses of Interface
pal.alignment.Alignment