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.datatype |
Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)
|
pal.eval |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
|
pal.substmodel |
Classes describing substitution models, i.e.
|
pal.treesearch |
Class | Description |
---|---|
CodonTable |
Describes a device for translating Nucleotide triplets
or codon indices into amino acid codes.
|
DataType |
interface for sequence data types
History: 21 March 2003, Added gap stuff, to counter frustration and not being
able to differentiat unknowns from gaps.
|
MolecularDataType |
An extension to the generic DataType class for DataTypes
related to genetic residues (by this it is meant Nucleotides,
AminoAcids, and Codons).
|
TransitionPenaltyTable |
Implements a table of transition penalties for a particular datatype.
|
Class | Description |
---|---|
AmbiguousDataType |
Additional interface information for data types which represent ambiguity in
sub types.
|
AminoAcids |
implements DataType for amino acids
|
Codons |
implements DataType for all Codons (including terminators).
|
CodonTable |
Describes a device for translating Nucleotide triplets
or codon indices into amino acid codes.
|
DataType |
interface for sequence data types
History: 21 March 2003, Added gap stuff, to counter frustration and not being
able to differentiat unknowns from gaps.
|
GapBalanced |
implements a ResidueDataType for GapBalanced notation.
|
IUPACNucleotides |
implements DataType for nucleotides with ambiguous characters
|
MolecularDataType |
An extension to the generic DataType class for DataTypes
related to genetic residues (by this it is meant Nucleotides,
AminoAcids, and Codons).
|
Nucleotides |
implements DataType for nucleotides
|
SimpleDataType |
interface for sequence data types
|
TransitionPenaltyTable |
Implements a table of transition penalties for a particular datatype.
|
TwoStates |
implements DataType for two-state data
|
Class | Description |
---|---|
DataType |
interface for sequence data types
History: 21 March 2003, Added gap stuff, to counter frustration and not being
able to differentiat unknowns from gaps.
|
Class | Description |
---|---|
CodonTable |
Describes a device for translating Nucleotide triplets
or codon indices into amino acid codes.
|
DataType |
interface for sequence data types
History: 21 March 2003, Added gap stuff, to counter frustration and not being
able to differentiat unknowns from gaps.
|
Class | Description |
---|---|
DataType |
interface for sequence data types
History: 21 March 2003, Added gap stuff, to counter frustration and not being
able to differentiat unknowns from gaps.
|