TreeOfLife.jl

TreeOfLife.jl

TreeOfLife.jl defines data types for cladograms and chronograms in phylogenetics and methods analyzing these trees.

In development.

Alternative packages include:

• Phylo.jl ("in beta", and its outdated prototype Phylogenetics.jl)
• PhyloTrees.jl
• TreeTools.jl
• Phylogenies.jl ("in development")

Examples

The followings are some simple examples illustrating the usage of this package. Please see the documentation for more details of TreeOfLife.jl.

julia> using TreeOfLife

julia> tree = fromnewick("(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;")
ChronoTree(ChronoNode[ChronoNode("F", 0, 0, 2, 0.0, 0.0), ChronoNode("A", 1, 3, 0, 0.1, 0.1), ChronoNode("B", 1, 4, 0, 0.2, 0.2), ChronoNode("E", 1, 0, 5, 0.5, 0.5), ChronoNode("C", 4, 6, 0, 0.8, 0.3), ChronoNode("D", 4, 0, 0, 0.9, 0.4)])

julia> tonewick(tree)
"(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;"

julia> tipnames = gettipnames(tree)
4-element Vector{String}:
 "A"
 "B"
 "C"
 "D"

julia> getmrca(tree, tipnames)
1

julia> getphylodiv(tree, tipnames)
1.5

julia> ismonophyl(tree, ["A", "B"])
false

julia> ismonophyl(tree, ["C", "D"])
true

AbstractNode

Abstract supertype for ChronoNode and CladoNode.

ChronoNode <: AbstractNode

Type for nodes in a ChronoTree. Compare CladoNode.

CladoNode <: AbstractNode

CladoNode(node::ChronoNode) :: CladoNode

Type for nodes in a CladoTree.

A ChronoNode can be converted to a CladoNode by removing all information about time.

AbstractTree

Abstract supertype for ChronoTree and CladoTree.

ChronoTree <: AbstractTree

ChronoTree(nodes::AbstractVector{ChronoNode}) :: ChronoTree
ChronoTree() :: ChronoTree

Type for chronograms or dated phylogenetic trees, assumed to be rooted, comprising ChronoNode instances. Compare CladoTree.

When called with no arguments, the constructor returns an empty ChronoTree.

CladoTree <: AbstractTree

CladoTree() :: CladoTree
CladoTree(nodes::AbstractVector{CladoNode}) :: CladoTree
CladoTree(tree::CladoTree) :: CladoTree
CladoTree(tree::ChronoTree) :: CladoTree

Type for cladograms or undated phylogenetic trees, assumed to be rooted, comprising CladoNode instances.

When called with no arguments, the constructor returns an empty CladoTree.

A ChronoTree can be converted to a CladoTree by removing all information about time.

length(tree::AbstractTree) :: Int

Return the number of nodes in a phylogenetic tree.

getindex(tree::AbstractTree, i) :: Any
getindex(tree::AbstractTree, i::Integer, trait::Symbol) :: Any
getindex(tree::AbstractTree, trait::Symbol) :: Dict{Int, <:Any}

Get the i-th node of the tree, or its trait, or a Dict containing the trait of all nodes of the tree. See also setindex!.

setindex!(tree::AbstractTree, node::AbstractNode, i::Integer) :: Vector
setindex!(tree::AbstractTree, tv, i::Integer, trait::Symbol) :: Dict

Set the i-th node of the tree or its trait. See also getindex.

haskey(tree::AbstractTree, trait::Symbol) :: Bool
haskey(tree::AbstractTree, i::Integer, trait::Symbol) :: Bool

Test if the tree or its i-th node has a trait or a trait value.

empty(tree::AbstractTree) :: AbstractTree

Construct a phylogenetic tree with only the root node of the same type.

==(node1::CladoNode, node2::CladoNode) :: Bool
==(node1::ChronoNode, node2::ChronoNode) :: Bool

Test if two nodes are identical, in the sense that they have the same name, the same parent, sibling, and child, as well as they have approximate branch lengths.

==(tree1::AbstractTree, tree2::AbstractTree) :: Bool

Test if two trees are identical, in the sense that they are of the same type, isomorphic, and have the same node ordering; specifically, for dated trees or ChronoTree instances, the node times are correspondingly equal.

Identical trees are always isomorphic (can be tested by isisomorph).

readnewick(filename::AbstractString) :: AbstractTree

Read a phylogenetic tree from disk. Compare writenewick.

readnewick(filename::AbstractString, tree::AbstractTree) :: AbstractTree

Write a phylogenetic tree to disk. Compare readnewick.

fromnewick(str::AbstractString; nocomments::Bool=false) :: AbstractTree

Create a phylogenetic tree from a Newick-format tree string.

Its inverse function is tonewick.

The argument nocomments controls whether the comments (enclosed by square brackets) are wiped out; by default it is set to false, i.e., all comments are kept.

tonewick(tree::CladoTree) :: String
tonewick(tree::ChronoTree) :: String

Express a phylogenetic tree as a Newick-format string.

Its inverse function is fromnewick.

ignore_comments(str::AbstractString) :: String

Remove comments enclosed by square brackets (possibly nested) in a string.

from_newick(str::AbstractString) :: Vector

Parse a Newick-format tree string into segments of different types according to their syntactical meanings. Used in fromnewick.

get_tree_type(elements::Vector) :: 
	Tuple{Type{<:AbstractTree}, Type{<:AbstractNode}}

Test whether a vector of elements parsed from some Newick-syntax tree string is a chronogram or a cladogram. Used in fromnewick.

to_newick!(elements::AbstractVector, 
	tree::CladoTree, i::Integer) :: AbstractVector
to_newick!(elements::AbstractVector, 
	tree::ChronoTree, i::Integer) :: AbstractVector

Convert a phylogenetic tree to segments of a Newick-format string. Used in tonewick.

readnexus(filename::AbstractString; every=0) :: Vector{ChronoTree}

Read dated phylogenetic trees from a Nexus-format file on disk.

gettips(tree::AbstractTree) :: Vector{Int}

Return the indices of all tip nodes of the tree.

gettipnames(tree::AbstractTree) :: Vector{String}

Return the names of all tip nodes of the tree.

alldistinct(tree::AbstractTree) :: Bool

Test if all tip nodes of the tree have distinct names.

getage(tree::ChronoTree; 
	average=mean_, getrelerr::Bool=false, reltol=1e-6) :: Float64

Return an average age (from the root node) of tip nodes of the tree.

The argument average defines the method for summarizing the ages to one; by default it is set to mean_.

The argument getrelerr controls whether the relative standard deviation is appended to the output ((mean, relstd)) or not (only mean); by default it is set to false.

The argument reltol is a tolerance of relative error. By default it is set to 1e-6. To suppress the judgment, set reltol=NaN.

getages(tree::ChronoTree; average=mean_, reltol=1e-6) :: Vector{Float64}

Return ages (from the root node) of all nodes of the tree.

The argument average defines the method for summarizing the ages to one; by default it is set to mean_.

The argument reltol is a tolerance of relative error. By default it is set to 1e-6. To suppress the judgment, set reltol=NaN.

getparent(tree::AbstractTree, i::Integer) :: Int

Find the parent or direct ancestor of tree[i] and return its index.

getchildren(tree::AbstractTree, i::Integer) :: Vector{Int}

Find all children or direct descendents of tree[i] and return their indices.

preorder(tree::AbstractTree, i=1) :: Vector{Int}

Return the pre-order traversal sequence of the whole tree, or its subtree with root node tree[i].

postorder(tree::AbstractTree, i=1) :: Vector{Int}

Return the post-order traversal sequence of the whole tree, or its subtree with root node tree[i].

isroot(tree::AbstractTree, i::Integer) :: Bool

Test if the i-th node of the tree is the root.

istip(tree::AbstractTree, i::Integer) :: Bool

Test if the i-th node of the tree is a tip or leaf node.

getname(node::AbstractNode) :: String
getname(tree::AbstractTree, i::Integer) :: String

Extract the name of the given node as a string.

hassibling(tree::AbstractTree, i::Integer) :: Bool

Test if the i-th node of the tree has following sibling(s).

rename(oldtree::AbstractTree, 
	oldtonew::Dict{<:AbstractString,<:AbstractString}

Create a new tree whose nodes are respectively renamed from the oldtree by a mapping from old names to new names. Specifically, nodes with empty names remain.

rename!(tree::Tree, 
	oldtonew::Dict{<:AbstractString,<:AbstractString}

Rename nodes of the tree in place by a mapping from old names to new names. Specifically, nodes with empty names remain.

getsubtree(oldtree::AbstractTree, tipset; 
	simplify::Bool=true, keeproot::Bool=false) :: AbstractTree

Extract the subtree generated from a given set of tips of the tree.

The argument simplify controls whether internal node with only one child needs to be reduced, i.e., connecting directly its child and its parent; by default it is set to true.

The argument keeproot controls whether the original root node needs to be contained in the subtree; by default it is set to false, in other words, yielding a truly minimum spanning tree (MST).

When simplify is set to false, the value of keeproot has no effect.

getmrca(tree::AbstractTree, tipset) :: Int

Find the index of the most recent common ancestor node for a set of nodes.

ismonophyl(tree::AbstractTree, tipset) :: Bool

Test if a given set of tip nodes are monophyletic based on the tree.

getphylodiv(tree::ChronoTree, tipset; keeproot::Bool=false)

Compute the phylogenetic diversity (PD) of a given set of tips of the tree, i.e., the sum of branch lengths of the subtree generated from the set.

The argument keeproot controls whether the original root node needs to be contained in the subtree; by default it is set to false.

cutfromroot(tree::ChronoTree, dist::Real; keep::Symbol=:both)
	:: Union{Vector{NTuple{2,Int}}, Vector{Int}}

Find the temporal section by dist time units after the root is born. The argument keep can be set among four options, i.e., :both (tuples containing parents and childs), :parent, :child, or :closer.

cutfromtips(tree::ChronoTree, dist::Real; 
	keep::Symbol=:both, average=minimum, reltol=1e-6) 
	:: Union{Vector{NTuple{2,Int}}, Vector{Int}}

Find the temporal section by dist time units before the root is born. The argument keep can be set among four options, i.e., :both (tuples containing parents and childs), :parent, :child, or :closer.

isbinary(tree::AbstractTree) :: Bool

Test if the tree is strictly binary or dichotonous, i.e., all non-tip nodes have exactly two descendents.

isisomorph(tree1::CladoTree, tree2::CladoTree) :: Bool
isisomorph(tree1::ChronoTree, tree2::ChronoTree) :: Bool

Test if two trees are isomorphic.

When both phylogenetic tree are dated, the isomorphism implies that branch lengths are correspondingly equal; otherwise, only the tree topology are compared.

getdescs(tree::AbstractTree, mrca::Int) :: Vector{Int}

Find the indices of all tip descendents from a common ancestor node.

getdescnames(tree::AbstractTree, mrca::Int) :: Vector{String}
getdescnames(tree::AbstractTree) :: Vector{Vector{String}}

Find the names of all tip descendents from a common ancestor node, or such descendent name lists for all nodes of the tree.

calibrate_t_root!(tree::ChronoTree) :: ChronoTree
calibrate_t_root!(tree::AbstractTree) :: AbstractTree

Calculate all t_root values according to t_branch values. Used in fromnewick.

calibrate_t_branch!(tree::ChronoTree) :: ChronoTree
calibrate_t_branch!(tree::AbstractTree) :: AbstractTree

Calibrate all t_root values of nodes of the tree so that the root's t_root is zero, and then recalculate all t_branch values according to the new t_root values. Used in getsubtree.

mean_(a::Vector{Float64}) :: Float64

Compute the arithmetic mean of a vector of 64-bit float numbers.

preorder!(sequence, tree::AbstractTree, i=1) :: Nothing

Append the pre-order traversal sequence of the whole tree, or its subtree with root node tree[i].

postorder!(sequence, tree::AbstractTree, i=1) :: Nothing

Append the post-order traversal sequence of the whole tree, or its subtree with root node tree[i].

get_selected(oldtree::AbstractTree, tipset; 
	simplify::Bool=true, keeproot::Bool=false) :: Vector{Int}

Select nodes of a subtree generated from a given set of tips of the tree. Used in getsubtree and isbinary.

Arguments simplify and keeproot have same meanings as in getsubtree.

sum_t_branch(tree::ChronoTree)

Compute the sum of branch lengths of the tree. Used in getphylodiv.

tree_hash(tree::CladoTree, h::UInt=zero(UInt)) :: UInt
tree_hash(tree::ChronoTree, h::UInt=zero(UInt)) :: UInt

Compute a hash value for a phylogenetic tree so that isomorphic trees necessarily have the same hash value (tested by isisomorph).

getconsensus(trees::Vector{<:AbstractTree}; 
	threshold::Float64=0.5, every::Int=0) :: CladoTree

Summarize phylogenetic trees to one such that clades with support rate no less than a threshold remain in the consensus tree.

The argument threshold should be a number between 0.5 and 1.0; the default value is 0.5.

The argument every, if set to a positive integer, makes the (probably long) analyzing process print a log per every trees; the default value is 0.

count_clade_ages(trees::Vector{ChronoTree}; every::Int=0) 
	:: Dict{Set{String}, Vector{Float64}}

Count the age for every possible tip node combination as long as occured at least once in some of the trees.

The argument every, if set to a positive integer, makes the (probably long) analyzing process print a log per every trees; the default value is 0.

count_clades(trees::Vector{<:AbstractTree}; every::Int=0)
	:: Dict{Set{String}, Int}

Count every possible tip node combination as long as occured at least once in some of the trees. Used in getconsensus.

The argument every, if set to a positive integer, makes the (probably long) analyzing process print a log per every trees; the default value is 0.

construct_tree(parents::Vector{Int}) :: Tuple{CladoTree, Int}

Construct a cladogram from parent indices. Used in getconsensus.