PhylogeneticTree (BioFSharp)

PhylogeneticTree Module

Namespace: BioFSharp
Assembly: BioFSharp.dll

Functions and values

Function or value	Description
`countBranches tree` Full Usage: `countBranches tree` Parameters: tree : `PhylogeneticTree<'T>` Returns: `int`	Returns the count of branches tree : `PhylogeneticTree<'T>` Returns: `int`
`countLeafs tree` Full Usage: `countLeafs tree` Parameters: tree : `PhylogeneticTree<'T>` Returns: `int`	Returns the count of leaves tree : `PhylogeneticTree<'T>` Returns: `int`
`fold folder acc tree` Full Usage: `fold folder acc tree` Parameters: folder : `'State -> 'T -> 'State` acc : `'State` tree : `PhylogeneticTree<'T>` Returns: `'State`	Iterates through a tree and accumulates a value by applying the folder to it and every branch and leaf. folder : `'State -> 'T -> 'State` acc : `'State` tree : `PhylogeneticTree<'T>` Returns: `'State`
`iter branchAction leafAction tree` Full Usage: `iter branchAction leafAction tree` Parameters: branchAction : `'T -> unit` leafAction : `'T -> unit` tree : `PhylogeneticTree<'T>`	Iterates trough a tree and performs an action on every branch and leaf branchAction : `'T -> unit` leafAction : `'T -> unit` tree : `PhylogeneticTree<'T>`
`map branchTagMapping leafTagMapping tree` Full Usage: `map branchTagMapping leafTagMapping tree` Parameters: branchTagMapping : `'T -> 'U` leafTagMapping : `'T -> 'U` tree : `PhylogeneticTree<'T>` Returns: `PhylogeneticTree<'U>`	Iterates trough a tree and transforms all branch and leaf values by applying a mapping function on them branchTagMapping : `'T -> 'U` leafTagMapping : `'T -> 'U` tree : `PhylogeneticTree<'T>` Returns: `PhylogeneticTree<'U>`
`ofHierarchicalCluster branchTag distanceConverter hCluster` Full Usage: `ofHierarchicalCluster branchTag distanceConverter hCluster` Parameters: branchTag : `'T` distanceConverter : `float -> 'Distance` hCluster : `Cluster<'T>` Returns: `PhylogeneticTree<'T * 'Distance>`	converts the input hierarchical clustering to a phylogenetig tree and conserves the distance insformation. In contrasr to the clustering result, the distance value of a Branch represents the distance to its Parent, not the distance that all children have to this Branch. branchTag : `'T` distanceConverter : `float -> 'Distance` hCluster : `Cluster<'T>` Returns: `PhylogeneticTree<'T * 'Distance>`
`ofTaggedBioSequences distanceFunction sequences` Full Usage: `ofTaggedBioSequences distanceFunction sequences` Parameters: distanceFunction : `'a seq -> 'a seq -> float` sequences : `TaggedSequence<string, 'a> seq` Returns: `PhylogeneticTree<TaggedSequence<string, 'a> * float>`	Performs hierarchical clustering of the input TaggedSequences using the provided distance function. Returns the result as a Phylogenetic tree. distanceFunction : `'a seq -> 'a seq -> float` sequences : `TaggedSequence<string, 'a> seq` Returns: `PhylogeneticTree<TaggedSequence<string, 'a> * float>`
`ofTaggedSequencesWithLinker branchTag distanceConverter distanceFunction linker sequences` Full Usage: `ofTaggedSequencesWithLinker branchTag distanceConverter distanceFunction linker sequences` Parameters: branchTag : `'T` distanceConverter : `float -> 'Distance` distanceFunction : `'S seq -> 'S seq -> float` linker : `LancWilliamsLinker` sequences : `TaggedSequence<'T, 'S> seq` Returns: `PhylogeneticTree<TaggedSequence<'T, 'S> * 'Distance>`	Performs hierarchical clustering of the input TaggedSequences using the provided distance function and linker. Returns the result as a Phylogenetic tree. branchTag : `'T` distanceConverter : `float -> 'Distance` distanceFunction : `'S seq -> 'S seq -> float` linker : `LancWilliamsLinker` sequences : `TaggedSequence<'T, 'S> seq` Returns: `PhylogeneticTree<TaggedSequence<'T, 'S> * 'Distance>`