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.