Uses of Interface
pal.misc.Report

Packages that use Report
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.mep
Classes for the analysis of "measurably evolving populations" (mep).
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.substmodel
Classes describing substitution models, i.e.
pal.supgma
 
pal.tree
Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).

  • Uses of Report in pal.alignment

    Subinterfaces of Report in pal.alignment
    Modifier and Type
    Interface
    Description
    interface 
    AnnotationAlignment
    The AnnotationAlignment interface is designed to provide annotation for an alignment.
    interface 
    CharacterAlignment
    This interface is designed to hold quantitative character states.
    Classes in pal.alignment that implement Report
    Modifier and Type
    Class
    Description
    class 
    AbstractAlignment
    abstract base class for any alignment data.
    class 
    BootstrappedAlignment
    generates bootstrapped alignments from a raw alignment
    class 
    ConcatenatedAlignment
    concatenates a list of alignments to one single alignment, increasing the number of sites
    class 
    ConcatenatedAnnotatedAlignment
    This is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences.
    class 
    GapBalancedAlignment
    Creates a "Gap-Balanced" alignment.
    class 
    IndelAlignment
    This class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms.
    class 
    IndelAnnotatedAlignment
    an extension of the IndelAlignment that includes annotation.
    class 
    JumbledAlignment
    generates jumbled alignments (randomizing input order of sequences)
    class 
    MultiLocusAnnotatedAlignment
    MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.
    class 
    ReadAlignment
    reads aligned sequence data from plain text files.
    class 
    ReadAlignmentOld
    reads aligned sequence data from plain text files.
    class 
    SimpleAlignment
    An alignment class that can be efficiently constructed from an array of strings.
    class 
    SimpleAnnotatedAlignment
    This is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment.
    class 
    SimpleCharacterAlignment
    This provides a basic implementation of CharacterAlignment.
    class 
    SitePattern
    takes an Alignment and determines its site patterns
    class 
    StrippedAlignment
    takes an alignment and repeatedly removes sites
    class 
    StrippedAnnotatedAlignment
    This is the stripped implementation of the Annotation interface, which is designed to provide stripped and annotated alignments.

  • Uses of Report in pal.coalescent

    Classes in pal.coalescent that implement Report
    Modifier and Type
    Class
    Description
    class 
    CoalescentIntervals
    A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.
    class 
    ConstantPopulation
    This class models coalescent intervals for a constant population (parameter: N0=present-day population size).
    class 
    ConstExpConst
    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.
    class 
    ConstExpGrowth
    This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.
    class 
    DemographicModel
    This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.
    class 
    ExpandingPopulation
    This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.
    class 
    ExponentialGrowth
    This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).
    class 
    SkylinePlot
    Skyline plot derived from a strictly bifurcating tree or a coalescent interval.

  • Uses of Report in pal.mep

    Classes in pal.mep that implement Report
    Modifier and Type
    Class
    Description
    class 
    ConstantMutationRate
    This class models a constant mutation rate (parameter: mu = mutation rate).
    class 
    MutationRateModel
    This abstract class contains methods that are of general use for modelling mutation rate changes over time.
    class 
    SteppedMutationRate
    This class models a step-wise mutation rate.
    class 
    WindowedMutationRate
    This class models a windowed mutation rate (parameter: mu = mutation rate).

  • Uses of Report in pal.statistics

    Classes in pal.statistics that implement Report
    Modifier and Type
    Class
    Description
    class 
    KishinoHasegawaTest
    Kishino-Hasegawa-(Templeton)-Test (1989, 1983) to compare a set of evolutionary hypotheses
    class 
    ModelSupport
    Computes Akaike weights and expected Akaike weights (relative evidence, expected relative evidence) for a set of models and computes corresponding confidence sets
    class 
    ShimodairaHasegawaTest
    Shimodaira-Hasegawa-Test (1999) to compare a set of evolutionary hypotheses

  • Uses of Report in pal.substmodel

    Subinterfaces of Report in pal.substmodel
    Modifier and Type
    Interface
    Description
    interface 
    RateMatrix
    abstract base class for all rate matrices
    interface 
    SubstitutionModel
    model of sequence substitution (rate matrix + rate variation).
    Classes in pal.substmodel that implement Report
    Modifier and Type
    Class
    Description
    class 
    AbstractRateMatrix
    abstract base class for all rate matrices
    class 
    AminoAcidModel
    base class of rate matrices for amino acids
    class 
    BLOSUM62
    BLOSUM62 model of amino acid evolution
    class 
    CachedRateMatrix
    a cached rate matrix.
    class 
    CodonModel
    base class for nucleotide rate matrices
    class 
    CPREV
    CPREV model of amino acid evolution (J.Adachi et al.
    class 
    Dayhoff
    Dayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.
    class 
    F81
    Felsenstein 1981 model of nucleotide evolution
    class 
    F84
    Felsenstein 1984 (PHYLIP) model of nucleotide evolution
    class 
    GammaRates
    discrete Gamma distribution (Z.
    class 
    GeneralRateDistributionSubstitutionModel
     
    class 
    GTR
    GTR (general time reversible) model of nucleotide evolution Lanave, C., G.
    class 
    HKY
    Hasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H.
    class 
    InvariableSites
    invariable sites model (two-rate model with mean rate = 1.0)
    class 
    JTT
    JTT model of amino acid evolution Jones, D.
    class 
    MTREV24
    MTREV24 model of amino acid evolution
    class 
    NucleotideModel
    base class for nucleotide rate matrices
    class 
    RateDistribution
    abstract base class for models of rate variation over sites employing a discrete rate distribution
    class 
    SingleClassSubstitutionModel
     
    class 
    TN
    Tamura-Nei model of nucleotide evolution Tamura, K.
    class 
    TwoStateModel
    implements the most general reversible rate matrix for two-state data
    class 
    UniformRate
    uniform rate distribution
    class 
    VT
    VT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T.
    class 
    WAG
    WAG model of amino acid evolution (S.
    class 
    YangCodonModel
    Yang's model of codon evolution More advanced codon Substitution Models (of Neilson and Yang) are now included (the M1, and M2 models).
    static class 
    YangCodonModel.SimpleNeutralSelection
    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.
    static class 
    YangCodonModel.SimplePositiveSelection
    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.

  • Uses of Report in pal.supgma

    Classes in pal.supgma that implement Report
    Modifier and Type
    Class
    Description
    class 
    SUPGMATree
    constructs an SUPGMA tree from pairwise distances.

  • Uses of Report in pal.tree

    Classes in pal.tree that implement Report
    Modifier and Type
    Class
    Description
    class 
    ClusterTree
     
    class 
    NeighborJoiningTree
    constructs a neighbor-joining tree from pairwise distances

    Saitou, N., and Nei, M., (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees.
    class 
    ReadTree
    constructs a tree reading in a New Hampshire treefile, taking care for internal labels and branch lengths and binary/nonbinary and rooted/unrooted trees
    class 
    SimpleTree
    data structure for a binary/non-binary rooted/unrooted trees
    class 
    SimulatedAlignment
    generates an artificial data set
    static class 
    Tree.TreeBase
     
    class 
    UPGMATree
    Deprecated.
    Use ClusterTree