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.
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Classes in pal.datatype used by pal.alignmentClassDescriptionDescribes 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.
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Classes in pal.datatype used by pal.datatypeClassDescriptionAdditional interface information for data types which represent ambiguity in sub types.implements DataType for amino acidsimplements 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 charactersAn extension to the generic DataType class for DataTypes related to genetic residues (by this it is meant Nucleotides, AminoAcids, and Codons).implements DataType for nucleotidesinterface for sequence data typesImplements a table of transition penalties for a particular datatype.implements DataType for two-state data
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Classes in pal.datatype used by pal.evalClassDescriptioninterface for sequence data types History: 21 March 2003, Added gap stuff, to counter frustration and not being able to differentiat unknowns from gaps.
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Classes in pal.datatype used by pal.substmodelClassDescriptionDescribes 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.
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Classes in pal.datatype used by pal.treesearchClassDescriptioninterface for sequence data types History: 21 March 2003, Added gap stuff, to counter frustration and not being able to differentiat unknowns from gaps.