| 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 | Description |
|---|---|---|
static SitePattern |
SitePattern.getSitePattern(Alignment a) |
| Modifier and Type | Method | Description |
|---|---|---|
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 |
AlignmentDistanceMatrix.recompute(SitePattern sp,
AlgorithmCallback callback) |
recompute observed distances under new site pattern
|
void |
PairwiseDistance.updateSitePattern(SitePattern sp) |
update site pattern
|
void |
SequencePairLikelihood.updateSitePattern(SitePattern sp) |
update site pattern
|
| Constructor | Description |
|---|---|
AlignmentDistanceMatrix(SitePattern sp) |
compute observed distances
|
AlignmentDistanceMatrix(SitePattern sp,
SubstitutionModel m) |
compute maximum-likelihood distances
|
AlignmentDistanceMatrix(SitePattern sp,
SubstitutionModel m,
AlgorithmCallback callback) |
compute maximum-likelihood distances
|
AlignmentDistanceMatrix(SitePattern sp,
AlgorithmCallback callback) |
compute observed 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 | Description |
|---|---|---|
SitePattern |
LikelihoodValue.getSitePattern() |
Returns the site pattern of this likelihood value
|
SitePattern |
SimpleLikelihoodCalculator.getSitePattern() |
| Modifier and Type | Method | Description |
|---|---|---|
void |
LikelihoodValue.renewSitePattern(SitePattern sp) |
Set new site pattern (while keeping tree and model)
|
void |
FastLikelihoodCalculator.updateSitePattern(SitePattern pattern) |
| Constructor | 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) |