Uses of Package
pal.datatype
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Packages that use pal.datatype 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 -
Classes in pal.datatype used by pal.alignment 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. -
Classes in pal.datatype used by pal.datatype Class Description AmbiguousDataType Additional interface information for data types which represent ambiguity in sub types.AminoAcids implements DataType for amino acidsCodons 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 charactersMolecularDataType 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 nucleotidesSimpleDataType interface for sequence data typesTransitionPenaltyTable 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 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. -
Classes in pal.datatype used by pal.substmodel 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. -
Classes in pal.datatype used by pal.treesearch 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.