Uses of Interface
pal.misc.Report

Packages that use Report
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
 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
 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
 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
 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
 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
 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
 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
 class SUPGMATree
          constructs an SUPGMA tree from pairwise distances.
 

Uses of Report in pal.tree
 

Classes in pal.tree that implement Report
 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