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Packages that use pal.datatype | |
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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 | |
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CodonTable
Describes a device for translating Nucleotide triplets or codon indices into amino acid codes. |
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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. |
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MolecularDataType
An extension to the generic DataType class for DataTypes related to genetic residues (by this it is meant Nucleotides, AminoAcids, and Codons). |
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TransitionPenaltyTable
Implements a table of transition penalties for a particular datatype. |
Classes in pal.datatype used by pal.datatype | |
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AmbiguousDataType
Additional interface information for data types which represent ambiguity in sub types. |
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AminoAcids
implements DataType for amino acids |
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Codons
implements DataType for all Codons (including terminators). |
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CodonTable
Describes a device for translating Nucleotide triplets or codon indices into amino acid codes. |
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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. |
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GapBalanced
implements a ResidueDataType for GapBalanced notation. |
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IUPACNucleotides
implements DataType for nucleotides with ambiguous characters |
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MolecularDataType
An extension to the generic DataType class for DataTypes related to genetic residues (by this it is meant Nucleotides, AminoAcids, and Codons). |
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Nucleotides
implements DataType for nucleotides |
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SimpleDataType
interface for sequence data types |
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TransitionPenaltyTable
Implements a table of transition penalties for a particular datatype. |
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TwoStates
implements DataType for two-state data |
Classes in pal.datatype used by pal.eval | |
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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 | |
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CodonTable
Describes a device for translating Nucleotide triplets or codon indices into amino acid codes. |
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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 | |
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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. |
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