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.distance |
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
|
pal.eval |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
|
Modifier and Type | Method and Description |
---|---|
static SitePattern |
SitePattern.getSitePattern(Alignment a) |
Modifier and Type | Method and Description |
---|---|
void |
AlignmentDistanceMatrix.recompute(SitePattern sp,
AlgorithmCallback callback)
recompute observed distances under new site pattern
|
void |
AlignmentDistanceMatrix.recompute(SitePattern sp,
SubstitutionModel model)
recompute maximum-likelihood distances under new site pattern
|
void |
AlignmentDistanceMatrix.recompute(SitePattern sp,
SubstitutionModel model,
AlgorithmCallback callback)
recompute maximum-likelihood distances under new site pattern
|
void |
SequencePairLikelihood.updateSitePattern(SitePattern sp)
update site pattern
|
void |
PairwiseDistance.updateSitePattern(SitePattern sp)
update site pattern
|
Constructor and Description |
---|
AlignmentDistanceMatrix(SitePattern sp)
compute observed distances
|
AlignmentDistanceMatrix(SitePattern sp,
AlgorithmCallback callback)
compute observed distances
|
AlignmentDistanceMatrix(SitePattern sp,
SubstitutionModel m)
compute maximum-likelihood distances
|
AlignmentDistanceMatrix(SitePattern sp,
SubstitutionModel m,
AlgorithmCallback callback)
compute maximum-likelihood distances
|
JukesCantorDistanceMatrix(SitePattern sitePattern)
compute jukes-cantor corrected distances
|
PairwiseDistance(SitePattern sp)
Constructor 1 (estimate observed distances only)
|
PairwiseDistance(SitePattern sp,
SubstitutionModel m)
Constructor 2 (uses evolutionary model)
|
SequencePairLikelihood(SitePattern sp,
SubstitutionModel m)
initialisation
|
Modifier and Type | Method and Description |
---|---|
SitePattern |
LikelihoodValue.getSitePattern()
Returns the site pattern of this likelihood value
|
SitePattern |
SimpleLikelihoodCalculator.getSitePattern() |
Modifier and Type | Method and Description |
---|---|
void |
LikelihoodValue.renewSitePattern(SitePattern sp)
Set new site pattern (while keeping tree and model)
|
void |
FastLikelihoodCalculator.updateSitePattern(SitePattern pattern) |
Constructor and Description |
---|
DemographicLikelihoodValue(SitePattern sp)
Parameter taking a site pattern.
|
FastLikelihoodCalculator(SitePattern pattern)
Constructor taking only site pattern.
|
FastLikelihoodCalculator(SitePattern pattern,
Tree tree,
RateMatrix model)
Constructor taking site pattern, tree and model.
|
LikelihoodValue(SitePattern sp)
initialization
|
ModelParameters(SitePattern sp,
SubstitutionModel m)
Constructor
|
SimpleLikelihoodCalculator(SitePattern pattern)
Need to use setTree(), and setModel() before using compute() if you use this constructor
|
SimpleLikelihoodCalculator(SitePattern pattern,
Tree tree,
RateMatrix model) |