Uses of Class
calhoun.analysis.crf.features.supporting.phylogenetic.PhylogeneticTreeFelsensteinOrder

Packages that use PhylogeneticTreeFelsensteinOrder

calhoun.analysis.crf.features.supporting.phylogenetic	utility classes for phylogenetic analysis
calhoun.analysis.crf.io	handles input and output of gene calling formats

Uses of PhylogeneticTreeFelsensteinOrder in calhoun.analysis.crf.features.supporting.phylogenetic

Methods in calhoun.analysis.crf.features.supporting.phylogenetic that return PhylogeneticTreeFelsensteinOrder

PhylogeneticTreeFelsensteinOrder

RootedBinaryPhylogeneticTree.getFelsensteinOrder(java.lang.String[] msaOrder) Given an ordering of species in a multiple alignment file, determine an order for computations by which Felsenstein's algorithm can be performed, and the branch lengths involved at each step.

Constructors in calhoun.analysis.crf.features.supporting.phylogenetic with parameters of type PhylogeneticTreeFelsensteinOrder

EvolutionaryModel(PhylogeneticTreeFelsensteinOrder T, double[] pi, NucleotideSubstitutionModel R)

Uses of PhylogeneticTreeFelsensteinOrder in calhoun.analysis.crf.io

Methods in calhoun.analysis.crf.io that return PhylogeneticTreeFelsensteinOrder

PhylogeneticTreeFelsensteinOrder

MultipleAlignmentInputSequence.getFelsensteinOrder()