Uses of Package
pal.datatype

Packages that use pal.datatype
Package
Description
Classes dealing with sequence alignments, including methods for reading and printing in several possible formats, as well as rearranging and concatenating.
Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)
Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.
Classes describing substitution models, i.e.
 
  • Classes in pal.datatype used by pal.alignment
    Class
    Description
    Describes a device for translating Nucleotide triplets or codon indices into amino acid codes.
    interface for sequence data types History: 21 March 2003, Added gap stuff, to counter frustration and not being able to differentiat unknowns from gaps.
    An extension to the generic DataType class for DataTypes related to genetic residues (by this it is meant Nucleotides, AminoAcids, and Codons).
    Implements a table of transition penalties for a particular datatype.
  • Classes in pal.datatype used by pal.datatype
    Class
    Description
    Additional interface information for data types which represent ambiguity in sub types.
    implements DataType for amino acids
    implements DataType for all Codons (including terminators).
    Describes a device for translating Nucleotide triplets or codon indices into amino acid codes.
    interface for sequence data types History: 21 March 2003, Added gap stuff, to counter frustration and not being able to differentiat unknowns from gaps.
    implements a ResidueDataType for GapBalanced notation.
    implements DataType for nucleotides with ambiguous characters
    An extension to the generic DataType class for DataTypes related to genetic residues (by this it is meant Nucleotides, AminoAcids, and Codons).
    implements DataType for nucleotides
    interface for sequence data types
    Implements a table of transition penalties for a particular datatype.
    implements DataType for two-state data
  • Classes in pal.datatype used by pal.eval
    Class
    Description
    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
    Class
    Description
    Describes a device for translating Nucleotide triplets or codon indices into amino acid codes.
    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
    Class
    Description
    interface for sequence data types History: 21 March 2003, Added gap stuff, to counter frustration and not being able to differentiat unknowns from gaps.