Uses of Interface
pal.alignment.Alignment

Packages that use Alignment
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
 interface AnnotationAlignment
          The AnnotationAlignment interface is designed to provide annotation for an alignment.
 

Classes in pal.alignment that implement Alignment
 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
protected  Alignment StrippedAlignment.rawAlignment
           
 

Methods in pal.alignment that return Alignment
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
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.newAlignment(Alignment a)
           
 void AlignmentReceiver.SingleReceiver.newAlignment(Alignment a)
           
 void AlignmentReceiver.BucketReceiver.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
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, Alignment b, java.lang.String guide1, java.lang.String guide2, char gap)
          This constructor combines to alignments given two guide strings.
SimpleAlignment(Alignment a, int sequenceToIgnore)
          Clone constructor.
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
 Alignment[] SerialCoalescentGenerator.Results.getAlignments()
           
 

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

Uses of Alignment in pal.distance
 

Methods in pal.distance with parameters of type Alignment
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 DistanceMatrixGenerator DistanceMatrixGenerator.Utils.createEvolutionary(Alignment a, SubstitutionModel sm)
           
static DistanceMatrixAccess DistanceMatrixAccess.Utils.createEvolutionary(Alignment a, SubstitutionModel sm)
           
 

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

Uses of Alignment in pal.eval
 

Methods in pal.eval that return Alignment
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
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
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
protected  Alignment LinkageDisequilibrium.theAlignment
           
 

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

Uses of Alignment in pal.tree
 

Classes in pal.tree that implement Alignment
 class SimulatedAlignment
          generates an artificial data set
 

Methods in pal.tree that return Alignment
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
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
 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
 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
 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
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
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
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.