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