Uses of Interface
pal.misc.Report
Packages that use Report
Package
Description
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
Classes to model population genetic processes using the coalescent.
Classes for the analysis of "measurably evolving populations" (mep).
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.)
Classes describing substitution models, i.e.
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.alignmentModifier and TypeInterfaceDescriptioninterface
The AnnotationAlignment interface is designed to provide annotation for an alignment.interface
This interface is designed to hold quantitative character states.Classes in pal.alignment that implement ReportModifier and TypeClassDescriptionclass
abstract base class for any alignment data.class
generates bootstrapped alignments from a raw alignmentclass
concatenates a list of alignments to one single alignment, increasing the number of sitesclass
This is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences.class
Creates a "Gap-Balanced" alignment.class
This class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms.class
an extension of the IndelAlignment that includes annotation.class
generates jumbled alignments (randomizing input order of sequences)class
MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.class
reads aligned sequence data from plain text files.class
reads aligned sequence data from plain text files.class
An alignment class that can be efficiently constructed from an array of strings.class
This is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment.class
This provides a basic implementation of CharacterAlignment.class
takes an Alignment and determines its site patternsclass
takes an alignment and repeatedly removes sitesclass
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 ReportModifier and TypeClassDescriptionclass
A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.class
This class models coalescent intervals for a constant population (parameter: N0=present-day population size).class
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
This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.class
This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.class
This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.class
This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).class
Skyline plot derived from a strictly bifurcating tree or a coalescent interval. -
Uses of Report in pal.mep
Modifier and TypeClassDescriptionclass
This class models a constant mutation rate (parameter: mu = mutation rate).class
This abstract class contains methods that are of general use for modelling mutation rate changes over time.class
This class models a step-wise mutation rate.class
This class models a windowed mutation rate (parameter: mu = mutation rate). -
Uses of Report in pal.statistics
Classes in pal.statistics that implement ReportModifier and TypeClassDescriptionclass
Kishino-Hasegawa-(Templeton)-Test (1989, 1983) to compare a set of evolutionary hypothesesclass
Computes Akaike weights and expected Akaike weights (relative evidence, expected relative evidence) for a set of models and computes corresponding confidence setsclass
Shimodaira-Hasegawa-Test (1999) to compare a set of evolutionary hypotheses -
Uses of Report in pal.substmodel
Subinterfaces of Report in pal.substmodelModifier and TypeInterfaceDescriptioninterface
abstract base class for all rate matricesinterface
model of sequence substitution (rate matrix + rate variation).Classes in pal.substmodel that implement ReportModifier and TypeClassDescriptionclass
abstract base class for all rate matricesclass
base class of rate matrices for amino acidsclass
BLOSUM62 model of amino acid evolutionclass
a cached rate matrix.class
base class for nucleotide rate matricesclass
CPREV model of amino acid evolution (J.Adachi et al.class
Dayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.class
Felsenstein 1981 model of nucleotide evolutionclass
Felsenstein 1984 (PHYLIP) model of nucleotide evolutionclass
discrete Gamma distribution (Z.class
class
GTR (general time reversible) model of nucleotide evolution Lanave, C., G.class
Hasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H.class
invariable sites model (two-rate model with mean rate = 1.0)class
JTT model of amino acid evolution Jones, D.class
MTREV24 model of amino acid evolutionclass
base class for nucleotide rate matricesclass
abstract base class for models of rate variation over sites employing a discrete rate distributionclass
class
Tamura-Nei model of nucleotide evolution Tamura, K.class
implements the most general reversible rate matrix for two-state dataclass
uniform rate distributionclass
VT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T.class
WAG model of amino acid evolution (S.class
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
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
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 ReportModifier and TypeClassDescriptionclass
constructs an SUPGMA tree from pairwise distances. -
Uses of Report in pal.tree
Modifier and TypeClassDescriptionclass
class
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
constructs a tree reading in a New Hampshire treefile, taking care for internal labels and branch lengths and binary/nonbinary and rooted/unrooted treesclass
data structure for a binary/non-binary rooted/unrooted treesclass
generates an artificial data setstatic class
class
Deprecated.Use ClusterTree