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## 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()`

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