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.

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

Uses of Interfacepal.misc.Report

Uses of Report in pal.alignment

Uses of Report in pal.coalescent

Uses of Report in pal.mep

Uses of Report in pal.statistics

Uses of Report in pal.substmodel

Uses of Report in pal.supgma

Uses of Report in pal.tree

Uses of Interface
pal.misc.Report