| 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.
|