| 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.substmodel |
Classes describing substitution models, i.e.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
AlignmentUtils.getPositionMisalignmentInfo(Alignment a,
java.io.PrintWriter out,
int startingCodonPosition,
CodonTable translator,
boolean removeIncompleteCodons) |
| Modifier and Type | Method and Description |
|---|---|
static CodonTable |
CodonTableFactory.createTranslator(int type)
Creates a translator of a given types
|
static CodonTable |
CodonTableFactory.createUniversalTranslator() |
| Modifier and Type | Method and Description |
|---|---|
static char[] |
CodonTableUtils.convertNucleotideToAminoAcid(char[] nucleotideSequence,
int startingPosition,
int length,
boolean reverse,
CodonTable translator)
Translates a Nucleotide sequence into a Amino Acid sequence
|
static java.lang.String |
CodonTableUtils.convertNucleotideToAminoAcid(java.lang.String nucleotideSequence,
int startingPosition,
int length,
boolean reverse,
CodonTable translator)
Translates a Nucleotide sequence into a Amino Acid sequence
|
| Constructor and Description |
|---|
GapBalanced(CodonTable translationTable) |
SpecificAminoAcids(CodonTable translationTable) |
| Constructor and Description |
|---|
NeutralSelectionRateMatrixGroup(MutableDouble kappaStore,
double[] freqs,
CodonTable table) |
PositiveSelectionRateMatrixGroup(MutableDouble kappaStore,
MutableDouble omegaStore,
double[] freqs,
CodonTable table) |
SimpleNeutralSelection(CodonTable translator,
double[] codonProbabilities,
double startingKappa) |
SimpleNeutralSelection(CodonTable translator,
double[] codonProbabilities,
double startingKappa,
double proportionZero) |
SimplePositiveSelection(CodonTable translator,
double[] codonProbabilities,
double startingKappa,
double startingFreeOmega) |
SimplePositiveSelection(CodonTable translator,
double[] codonProbabilities,
double startingKappa,
double startingFreeOmega,
double p0,
double p1) |
SimplePositiveSelection(CodonTable translator,
double[] codonProbabilities,
double startingKappa,
double startingFreeOmega,
double p0,
double p1,
double p2) |
YangCodonModel(double[] params,
double[] freq,
CodonTable codonTable)
constructor 3
|
YangCodonModel(double omega,
double kappa,
double[] freq,
CodonTable codonTable)
constructor 1
|