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

Packages that use RootedBinaryPhylogeneticTree

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

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

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

RootedBinaryPhylogeneticTree

RootedBinaryPhylogeneticTree.subtree(java.lang.String[] sn)

Uses of RootedBinaryPhylogeneticTree in calhoun.analysis.crf.io

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

RootedBinaryPhylogeneticTree	MultipleAlignmentInputSequence.getTree()
RootedBinaryPhylogeneticTree	MultipleAlignmentInputSequence.MultipleAlignmentColumn.getTree() returns the tree for this alignment

Constructors in calhoun.analysis.crf.io with parameters of type RootedBinaryPhylogeneticTree

MultipleAlignmentInputSequence(java.util.List<java.lang.String> speciesNames, java.util.List<java.lang.String> consensuses, java.lang.String refSpecies, RootedBinaryPhylogeneticTree tree)
constructs a multiple alignment input sequence.

MultipleAlignmentInputSequence(java.lang.String refSpecies, RootedBinaryPhylogeneticTree tree)

Uses of RootedBinaryPhylogeneticTree in calhoun.analysis.crf.test

Methods in calhoun.analysis.crf.test that return RootedBinaryPhylogeneticTree

static RootedBinaryPhylogeneticTree	ExampleTrees.bigTree()
static RootedBinaryPhylogeneticTree	ExampleTrees.bigTreeForEncode()
static RootedBinaryPhylogeneticTree	ExampleTrees.crypto4dan()
static RootedBinaryPhylogeneticTree	ExampleTrees.crypto5()