Phylogenetic trees in Julia
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README.md

PhyloTrees.jl

Build Status

Introduction

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

Installation

Pkg.add("PhyloTrees")

To enable plotting, install Plots.jl and one of its supported backends.

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.

Trees can be plotted using plot.

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