Index

Modules: phylogeni/io/parseNewick, phylogeni/io/writeNewick, phylogeni/simulate, phylogeni/tree.

API symbols

`$`:

• tree: `$`[T](node: Node[T]): string
• tree: `$`[T](tree: Tree[T]): string

addChild:

• tree: addChild[T](parent: Node[T]; newChild: Node[T])

addSister:

• tree: addSister[T](node: Node[T]; newSister: Node[T])

ascii:

• tree: ascii[T](node: Node[T]; char1 = "-"; showInternal = true): string
• tree: ascii[T](tree: Tree[T]; char1 = "-"; showInternal = true): string

calcTreeLength:

• tree: calcTreeLength[T](node: Node[T]; includeRoot = true): float
• tree: calcTreeLength[T](tree: Tree[T]): float

hash:

• tree: hash[T](n: Node[T]): Hash

inorder:

• tree: inorder[T](root: Node[T]): Node[T]
• tree: inorder[T](tree: Tree[T]): Node[T]

isLeaf:

• tree: isLeaf[T](node: Node[T]): bool

iterleaves:

• tree: iterleaves[T](root: Node[T]): Node[T]
• tree: iterleaves[T](tree: Tree[T]): Node[T]

ladderize:

• tree: ladderize[T](root: Node[T]; order: SortOrder = Ascending)
• tree: ladderize[T](tree: Tree[T]; order: SortOrder = Ascending)

levelorder:

• tree: levelorder[T](root: Node[T]): Node[T]
• tree: levelorder[T](tree: Tree[T]): Node[T]

NewickError:

• parseNewick: NewickError

newickorder:

• tree: newickorder[T](root: Node[T]): tuple[node: Node[T], firstVisit: bool]
• tree: newickorder[T](tree: Tree[T]): tuple[node: Node[T], firstVisit: bool]

NewickParser:

• parseNewick: NewickParser

newNode:

• tree: newNode(label: string; length: float; typ: typedesc = void): Node[typ]

newTree:

• tree: newTree(typ: typedesc = void): Tree[typ]

Node:

• tree: Node

parseNewickFile:

• parseNewick: parseNewickFile[T](tree: var Tree[T]; path: string)
• parseNewick: parseNewickFile[T](treeSeq: var TreeSeq[T]; path: string)

parseNewickStream:

• parseNewick: parseNewickStream[T](tree: var Tree[T]; stream: Stream)
• parseNewick: parseNewickStream[T](treeSeq: var TreeSeq[T]; stream: Stream)

parseNewickString:

• parseNewick: parseNewickString[T](tree: var Tree[T]; str: string)
• parseNewick: parseNewickString[T](treesSeq: var TreeSeq[T]; str: string)

postorder:

• tree: postorder[T](root: Node[T]): Node[T]
• tree: postorder[T](tree: Tree[T]): Node[T]

preorder:

• tree: preorder[T](root: Node[T]): Node[T]
• tree: preorder[T](tree: Tree[T]): Node[T]

prune:

• tree: prune[T](tree: Tree[T]; node: Node[T])
• tree: prune[T](tree: Tree[T]; nodes: seq[Node[T]])

Tree:

• tree: Tree

TreeError:

• tree: TreeError

treeFromFile:

• tree: treeFromFile(path: string; typ: typedesc = void): Tree[typ]

treeFromString:

• tree: treeFromString(str: string; typ: typedesc = void): Tree[typ]

treeHeight:

• tree: treeHeight[T](node: Node[T]; includeRoot = true): float
• tree: treeHeight[T](tree: Tree[T]; includeRoot = true): float

TreeSeq:

• tree: TreeSeq

uniformBirthDeath:

• simulate: uniformBirthDeath(nTips: int; birthRate = 1.0; deathRate = 1.0; rerun = false; typ = void): Tree[typ]

uniformPureBirth:

• simulate: uniformPureBirth(nTips: int; birthRate: float = 1.0; typ = void): Tree[typ]

writeNewickFile:

• writeNewick: writeNewickFile[T](tree: Tree[T]; filename: string)

writeNewickString:

• writeNewick: writeNewickString[T](tree: Tree[T]): string