All Classes and Interfaces

Class
Description
abstract base class for any alignment data.
 
 
abstract base class for all rate matrices
 
A Utility class that provides some simple implementations of AlgorithmCallback that can be used for manipulating callback results
interface for any alignment data.
A class for the gradual construction of an alignment.
compute distance matrix (observed and ML) from alignment (SitePattern)
A AlignmentGenerator is an object that can generate alignments! (most probably replicates for statistical tests)
 
Exception thrown by ReadAlignment
Temporary class for reading alignments...
 
 
 
The SingleReceiver only keeps track of one alignment, the last one it received
The SingleReceiver only keeps track of one alignment, the last one it received
Simple access for alignment functions.
Helper utilities for alignments.
Additional interface information for data types which represent ambiguity in sub types.
base class of rate matrices for amino acids
interface for IDs of amino acid models
implements DataType for amino acids
The AnnotationAlignment interface is designed to provide annotation for an alignment.
Title:
An immutable attribute has a name and value.
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree.
Binomial coefficients
BLOSUM62 model of amino acid evolution
generates bootstrapped alignments from a raw alignment
computation of bootstrap estimators (BIAS, SD, VAR, CI) given a statistic theta and corresponding bootstrap replicates.
returns a very large number instead of the function value if arguments are out of bound (useful for minimization with minimizers that don't check argument boundaries)
 
 
limits for branch lengths
a cached rate matrix.
This interface is designed to hold quantitative character states.
chi-square distribution (distribution of sum of squares of n uniform random variables) (Parameter: n; mean: n; variance: 2*n) The chi-square distribution is a special case of the Gamma distribution (shape parameter = n/2.0, scale = 2.0).
chi-square test
computes chi-square value of a (parameterized) tree for its set of parameters (e.g., branch lengths) and a given distance matrix
 
data structure for a set of splits
 
provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)
 
An interface for describing Clustering methods To be updated to cope with Ward's method and others...
Exceptions to do with coalescent models et cetera.
A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.
Simulates a set of coalescent intervals given a demographic model.
interface defining a parameterized tree that includes demographic information.
base class for nucleotide rate matrices
implements DataType for all Codons (including terminators).
Describes a device for translating Nucleotide triplets or codon indices into amino acid codes.
Generates CodonTables
Nucleotide Translating Utilities
interface for an object that is comparable.
This class is unfortunate but necessary to conform to JDK 1.1
interface for an object that can compare other objects for the purposes of ordering them.
concatenates a list of alignments to one single alignment, increasing the number of sites
This is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences.
Title: ConditionalProbabilityStore (was ConditionalLikelihoodStore)
 
methods for minimization of a real-valued function of several variables without using derivatives (Brent's modification of a conjugate direction search method proposed by Powell)
minimization of a real-valued function of several variables using a the nonlinear conjugate gradient method where several variants of the direction update are available (Fletcher-Reeves, Polak-Ribiere, Beale-Sorenson, Hestenes-Stiefel) and bounds are respected.
Title: ConstantIndependentSingleSplitDistribution
This class models a constant mutation rate (parameter: mu = mutation rate).
This class models coalescent intervals for a constant population (parameter: N0=present-day population size).
Title: Constants
This class models a population that grows exponentially from an initial population size alpha N0 at time y to a size N0 at time x until the present-day.
This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.
 
 
 
 
 
 
Class for permuting contigency tables and determining the likelihood of the table.
CPREV model of amino acid evolution (J.Adachi et al.
 
interface for sequence data types History: 21 March 2003, Added gap stuff, to counter frustration and not being able to differentiat unknowns from gaps.
Some useful methods for implmenting classes and for DataType users
Simple access for data type functions.
Dayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.
 
 
 
 
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).
Estimates the likelihood for a tree using a specified model of sequence evolution and a sequence alignment and a specific demographic model as a prior on coalescent intervals.
This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.
interface defining a parameterized tree that includes demographic information.
estimates demographic parameters by maximising the coalescent prior for a tree with given branch lengths.
global minimization of a real-valued function of several variables without using derivatives using a genetic algorithm (Differential Evolution)
simple discrete statistics (mean, variance, cumulative probability, quantiles etc.)
storage for pairwise distance matrices.
 
 
 
 
Auxillary functions for distance matrices
exception thrown by ReadDistanceMatrix
 
 
 
This class provides static methods for creating DOM Elements from PAL Objects.
This class provides static methods for parsing PAL objects from DOM Elements.
error function and related stuff
A utiltity class that can be used to track the number of evaluations of a general function
This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.
exponential distribution.
This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).
Defines objects that listen to exteneral ParameterEvents
Felsenstein 1981 model of nucleotide evolution
Felsenstein 1984 (PHYLIP) model of nucleotide evolution
 
Title: Fast Likelihood Calculator
Description: A fast likelihood calculator
Original code by Matthew Goode.
This does a one tail fisher exact test.
 
 
tools to simplify formatted input from an input stream
tools to simplify formatted output to a stream
 
 
 
 
gamma distribution.
gamma function
discrete Gamma distribution (Z.
implements a ResidueDataType for GapBalanced notation.
Creates a "Gap-Balanced" alignment.
 
 
 
 
Provides an general interface to the DifferentialEvolution class that is not tied to a certain number of parameters (as DifferentialEvolution is).
Title: General Likelihood Calculator
Description: A General likelihood calculator
This calculates the likelihood of an topologically invariant tree (on an unchanging alignment) quickly by remembering partial likelihoods of invariant subtrees, and by essentially generating site patterns for each sub tree.
 
Title:
 
A general rate matrix class for JC69/F81 style rate matrices (but for all data types)
 
A general rate matrix class for REV style rate matrices (GTR but for all data types) Includes the ability for arbitarily constraints
 
 
This class provides from genotype to be constructed from separate but paired alignments.
 
Title: GroupLeader
GTR (general time reversible) model of nucleotide evolution Lanave, C., G.
sorts numbers and comparable objects by treating contents of array as a binary tree.
Title: HeightInformationUser
Hasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H.
An identifier for some sampled data.
Generates IdGroup objects given certain parameters.
An indexed group of identifiers.
 
This class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms.
an extension of the IndelAlignment that includes annotation.
Title:
 
 
convenience class to open input streams linked to files, stdin, and strings
A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.
invariable sites model (two-rate model with mean rate = 1.0)
implements DataType for nucleotides with ambiguous characters
Implements a table of transition penalties for a DNA states and IUPAC ambiguous states.
JTT model of amino acid evolution Jones, D.
compute jukes-cantor corrected distance matrix
generates jumbled alignments (randomizing input order of sequences)
Kishino-Hasegawa-(Templeton)-Test (1989, 1983) to compare a set of evolutionary hypotheses
A Label display object displays a label at a particular location on a graphics object.
 
 
 
 
 
 
The External calculator does not maintain any state and is approapriate for calculation where a store is provided
 
 
The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structure
A LHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.
classes that calculate likelihoods should implement this interface.
 
 
 
 
 
Likelihood ratio test based on chi-square statistics
 
 
Computes the likelihood for a tree given a model of sequence evolution and a sequence alignment; also optimises tree parameters such as branch lengths by maximising the likelihood (for optimal performance special optimisation procedures are employed for UnconstrainedTree, ClockTree and DatedTipsClockTree; a general optimisation precedure is used for another ParameterizedTree).
converts a multivariate function into a univariate function
This class calculates D' and r^2 estimates of linkage disequilibrium.
An AWT Component for displaying information on linkage disequilibrium.
Title: LMSSolver
Title: Utils
Implements LOCAL (Larget and Simon, 1999) and stochastic NNI moves for unrooted trees.
Log provides a mechanism for logging and debugging to the standard output stream.
Interface for all objects that provide a logging facility.
This class logarithmically transforms tree parameters.
determines machine accuracy
Title: Markable
Handy utility functions which have some Mathematical relavance.
Title: Matrix
compute matrix exponential and, subsequently, transition probabilities for a given rate matrix
MersenneTwisterFast: A simulation quality fast random number generator (MT19937) with the same public methods as java.util.Random.
interface for a function of several variables with a gradient
interface for a classes that wish to monitor the progress of a Minimiser
 
estimates substitution model parameters from the data
Computes Akaike weights and expected Akaike weights (relative evidence, expected relative evidence) for a set of models and computes corresponding confidence sets
 
The External calculator does not maintain any state and is approapriate for calculation where a store is provided
 
 
The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structure
A ConstrainedLHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.
 
An extension to the generic DataType class for DataTypes related to genetic residues (by this it is meant Nucleotides, AminoAcids, and Codons).
Utilities relating to MolecularDataType stuff
 
MTREV24 model of amino acid evolution
MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.
Title: MultiParameterized
An interface for classes that wish to find out about particular parameter access
 
interface for a function of several variables
abstract base class for minimisation of a multivariate function
A factory interface for MultivariateMinimums (because they aren't statefree)
 
This abstract class contains methods that are of general use for modelling mutation rate changes over time.
An interface for objects which generate fresh MutationRAteModels
Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).
interface for classes that can be named.
 
interface for class with (optimizable) named parameters
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.
interface for class with (optimizable) parameters.
The new RateMatrix class.
 
Exception class for the NexusParser.
Comments
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree
 
 
Helper routines for dealing with nodes.
normal distribution (pdf, cdf, quantile)
base class for nucleotide rate matrices
interface for IDs of nucleotide models
implements DataType for nucleotides
approximates numerically the first and second derivatives of a function of a single variable and approximates gradient and diagonal of Hessian for multivariate functions
This datatype stores numeric values.
Title: Object State
A means for describing odering information, and Utilities for creating such Orderings
 
 
Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum) hints about the function that may alow it to optimise better.
 
converts a multivariate function into a univariate function by keeping all but one argument constant
minimization of a real-valued function of several variables without using derivatives, using the simple strategy of optimizing variables one by one.
 
convenience class to create output streams linked to files, stdout, and strings
An interface for objects which are used for painting themselves in a general Graphics object
determines the (observed and ML) distance between a pair of sequences
A utility class for accomodating Pal listeners
An event used by PalObjectListeners
Defines objects that monitor certain PalObjects for changes
A base class for classes that fire PalObject events
An event used by ExternalParameterListeners
interface for class with (optimizable) parameters
NullParameterized Object Can be used by subclasses to implement parameterized without actually having paramters
A Utility class for using as the superclass to subclasses which are based on double arrays
A Utility class for using as the superclass to subclasses which work by adding functionality to a general Parameterized object (the base Parameterized object)
 
Title: ParameterizedDoubleBundle
Title: ParameterizedNeoWrapper
abstract base class for a tree with an Parameterized interface
Factory interface
For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)
 
Pareto distribution (scale-free distribution without characteristic length scale).
Title: PatternInfo
Penalized likelihood criteria
 
A tree node that has a scalar position for the purposes of drawing the tree.
 
A function for obtaining probabilities (that may change over time)
 
 
Title: Ranker Description: Maintains a list of ranked objects
abstract base class for models of rate variation over sites employing a discrete rate distribution
 
 
abstract base class for all rate matrices
 
 
 
reads aligned sequence data from plain text files.
reads aligned sequence data from plain text files.
reads pairwise distance matrices in PHYLIP format (full matrix)
constructs a tree reading in a New Hampshire treefile, taking care for internal labels and branch lengths and binary/nonbinary and rooted/unrooted trees
release information
 
 
 
interface for classes that can print out a human readable report of itself
 
Title: RootedTreeInterface
 
 
 
 
This class contains utility methods.
Title: SampleInformation
 
Title: SaturatedSingleSplitDistribution
A simplistic class (most of the work is done elsewhere) that handles basic search algorithms
 
Title: SearchMonitor
 
computation of the (negative) log-likelihood for a pair of sequences
 
 
A simple wrapper class for containing the results which may either be a number of trees, or a number of trees and alignments (in parallel arrays)
Simulates a set of coalescent intervals given a demographic model.
Title: ShimodairaHasegawaStatistics
Shimodaira-Hasegawa-Test (1999) to compare a set of evolutionary hypotheses
An alignment class that can be efficiently constructed from an array of strings.
This is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment.
This provides a basic implementation of CharacterAlignment.
interface for sequence data types
Default implementation of IdGroup interface.
 
 
 
 
 
data structure for a node (includes branch) in a binary/non-binary rooted/unrooted tree
 
 
data structure for a binary/non-binary rooted/unrooted trees
 
 
 
generates an artificial data set
A utility class that can be used to generate Simulated alignments based on a tree with predefined sequence length and substitution model
 
 
 
 
 
takes an Alignment and determines its site patterns
Skyline plot derived from a strictly bifurcating tree or a coalescent interval.
implements a MolecularDataType for amino acids, where we specifiy the Codon Table basis of amino acid by supplying the CodonTable which is/was used for converting Nucleotide sequences to Amino Acids.
data structure for a set of splits
utilities for split systems
 
Title:
A standard data type, but with characters removed
This class models a step-wise mutation rate.
 
 
 
takes an alignment and repeatedly removes sites
This is the stripped implementation of the Annotation interface, which is designed to provide stripped and annotated alignments.
model of sequence substitution (rate matrix + rate variation).
A small Utility class for things relating to Substitution Models in general
 
interface for classes that can provide summaries
 
 
 
Corrects distances in a distance matrix such that all tips appear contemporaneous, given a time/date and rate information for the taxa.
constructs an SUPGMA tree from pairwise distances.
interface for classes with data that can be presented in tables
 
 
 
 
sorts three numbers (doubles) and choose randomly among the minimum/maximum values
Character data that expresses an order through time.
keeps track of program runtime
Tamura-Nei model of nucleotide evolution Tamura, K.
Title: TOCDSampleInformation
 
 
 
 
Implements a table of transition penalties for a particular datatype.
For objects that represent a source of transition probabilities TransitionProbability.java,v 1.3 2000/08/08 22:58:29 alexi Exp $
Interface for a phylogenetic or genealogical tree.
 
An AWT Component for displaying a tree.
computes distance matrix induced by a tree (needs only O(n^2) time, following algorithm DistanceInTree by D.Bryant and P.
 
 
 
 
The branch access objects allow specific operations on a particular branch (refered to as connections internally to confuse and bewilder)
 
 
Title: TreeOperation
Utility class
A class that can paint a tree into a Graphics object.
A class that can paint a tree (in a circular fashion) into a Graphics object .
A class that can paint a tree into a Graphics object.
exception thrown by ReadTree
 
Title: TreeSearchTool
 
various utility functions on trees.
implements the most general reversible rate matrix for two-state data
implements DataType for two-state data
 
The External calculator does not maintain any state and is approapriate for calculation where a store is provided
 
The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structure
A LHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.
 
provides parameter interface to an unconstrained tree (parameters are all available branch lengths)
 
 
uniform rate distribution
interface holding unit constants
interface for classes that can provide the related Units used, (as
interface for a function of one variable
minimization of a real-valued function of one variable without using derivatives.
 
 
Title: UnrootedTreeInterface
 
 
 
 
 
 
Deprecated.
Use ClusterTree
class for drawing numbers from an urn with and without laying back
Provides some miscellaneous methods.
Title: VariableIndependentSingleSplitDistribution
This class provides a mechanism for returning the version number of the pal library.
VT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T.
WAG model of amino acid evolution (S.
This class models a windowed mutation rate (parameter: mu = mutation rate).
constants (strings and numbers) relating to reading and writing XML.
exception thrown by ElementParser.
Yang's model of codon evolution More advanced codon Substitution Models (of Neilson and Yang) are now included (the M1, and M2 models).
A Substitution Model which can be used to implment the Neutral Model (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of trwo base YangCodon models where omega=0, omega=1 repectively
[1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene.
A Substitution Model which can be used to implment the Postitive Selection (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of a three base Codon model where omega=0, omega=1 and omega=free
[1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene.
A Utility class