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PhyloTrees

Phylogenetic trees in Julia

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PhyloTrees.jl

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Introduction

The objective of PhyloTrees.jl is to provide fast and simple tools for working with rooted phylogenetic trees in Julia.

Installation

Julia 1.0.x, 1.1.x, and 1.2.x are currently supported. The current release can be installed from the Julia REPL:

pkg> add PhyloTrees

The development version (master branch) can be installed as:

pkg> add PhyloTrees#master

Usage

There are several ways to add nodes and branches to our Tree, see below for examples

> # Initialize the tree
> exampletree = Tree()

Phylogenetic tree with 0 nodes and 0 branches

> # Add a node to the tree
> addnode!(exampletree)

Phylogenetic tree with 1 nodes and 0 branches

Branches have Float64 lengths

> # Add a node, connect it to node 1 with a branch 5.0 units in length
> branch!(exampletree, 1, 5.0)

Phylogenetic tree with 2 nodes and 1 branches

> # Add 2 nodes
> addnodes!(exampletree, 2)

Phylogenetic tree with 4 nodes and 1 branches

> # Add a branch from node 2 to node 3 10.0 units in length
> addbranch!(exampletree, 2, 3, 10.0)

Phylogenetic tree with 4 nodes and 2 branches

We can quickly look at the nodes present in our Tree:

> collect(exampletree.nodes)

[unattached node]
[branch 1]-->[internal node]-->[branch 2]
[branch 2]-->[leaf node]                 
[root node]-->[branch 1]

Other capabilities

Distance between nodes can be calculated using the distance function. A node visit ordering for postorder traversal of a tree can be found with postorder.

There are many other functions available that are helpful when dealing with trees including: changesource!, changetarget!, indegree, outdegree, isroot, isleaf, isinternal, findroots, findleaves, findinternal, findnonroots, findnonleaves, findexternal, areconnected, nodepath, branchpath, parentnode, childnodes, descendantcount, descendantnodes, ancestorcount, ancestornodes, and nodetype.

First Commit

03/02/2016

Last Touched

3 months ago

Commits

170 commits

Requires:

Used By: