TreeKnit

TreeKnit is a julia package that performs inference of reassortment events in segmented genomes, such as human influenza. Additionally, it can reconstruct Ancestral Reassortment Graphs for segment pairs.

Installation

TreeKnit requires Julia version 1.7, it may not work with higher or lower versions. You can get v1.7.3 of Julia here. Alternatively, you can install julia 1.7.3 into a conda environment.

You can install TreeKnit using the julia package manager:

using Pkg
Pkg.add("TreeKnit")

You should now be able to use using TreeKnit from inside julia.

TreeTools package

If you are going to use TreeKnit from inside a julia session, you will very likely need the TreeTools package to read Newick tree files in a format that TreeKnit takes as input. You can get TreeTools by typing Pkg.add("TreeTools") from a julia console.

To use the CLI (Linux/Mac users), build the package by calling

using Pkg
Pkg.build("TreeKnit")

This will add executable scripts to your ~/.julia/bin folder. Simply add this folder to your path to call the script, e.g. export PATH="$HOME/.julia/bin:$PATH". You should now be able to call, e.g., treeknit --help.