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Packages that use Report | |
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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 |
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Subinterfaces of Report in pal.alignment | |
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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 | |
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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 |
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Classes in pal.coalescent that implement Report | |
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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 |
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Classes in pal.mep that implement Report | |
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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 |
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Classes in pal.statistics that implement Report | |
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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 |
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Subinterfaces of Report in pal.substmodel | |
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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 | |
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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
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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
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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 |
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Classes in pal.supgma that implement Report | |
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class |
SUPGMATree
constructs an SUPGMA tree from pairwise distances. |
Uses of Report in pal.tree |
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Classes in pal.tree that implement Report | |
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class |
ClusterTree
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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
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class |
UPGMATree
Deprecated. Use ClusterTree |
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