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).
|
Modifier and Type | Interface and 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.
|
Modifier and Type | Class and 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.
|
Modifier and Type | Class and 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.
|
Modifier and Type | Class and 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).
|
Modifier and Type | Class and 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
|
Modifier and Type | Interface and Description |
---|---|
interface |
RateMatrix
abstract base class for all rate matrices
|
interface |
SubstitutionModel
model of sequence substitution (rate matrix + rate variation).
|
Modifier and Type | Class and 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. |
Modifier and Type | Class and Description |
---|---|
class |
SUPGMATree
constructs an SUPGMA tree from pairwise distances.
|
Modifier and Type | Class and 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
|