Uses of Package
pal.datatype

Packages that use pal.datatype

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

Classes in pal.datatype used by pal.alignment

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.

Classes in pal.datatype used by pal.datatype

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

Classes in pal.datatype used by pal.eval

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.

Classes in pal.datatype used by pal.substmodel

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.

Classes in pal.datatype used by pal.treesearch

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.