Uses of Interface
pal.misc.Report
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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). -
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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 alignmentclass
ConcatenatedAlignment
concatenates a list of alignments to one single alignment, increasing the number of sitesclass
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 patternsclass
StrippedAlignment
takes an alignment and repeatedly removes sitesclass
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 hypothesesclass
ModelSupport
Computes Akaike weights and expected Akaike weights (relative evidence, expected relative evidence) for a set of models and computes corresponding confidence setsclass
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 matricesinterface
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 matricesclass
AminoAcidModel
base class of rate matrices for amino acidsclass
BLOSUM62
BLOSUM62 model of amino acid evolutionclass
CachedRateMatrix
a cached rate matrix.class
CodonModel
base class for nucleotide rate matricesclass
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 evolutionclass
F84
Felsenstein 1984 (PHYLIP) model of nucleotide evolutionclass
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 evolutionclass
NucleotideModel
base class for nucleotide rate matricesclass
RateDistribution
abstract base class for models of rate variation over sites employing a discrete rate distributionclass
SingleClassSubstitutionModel
class
TN
Tamura-Nei model of nucleotide evolution Tamura, K.class
TwoStateModel
implements the most general reversible rate matrix for two-state dataclass
UniformRate
uniform rate distributionclass
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 treesclass
SimpleTree
data structure for a binary/non-binary rooted/unrooted treesclass
SimulatedAlignment
generates an artificial data setstatic class
Tree.TreeBase
class
UPGMATree
Deprecated.Use ClusterTree
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