Skip to content

Workshop Requirements

Jump to bottom Edit New page
Cecile Ane edited this page Jul 6, 2018 · 3 revisions

Operating System

We will support Linux and Mac during the workshop. Julia runs on Windows, but far less smoothly so Windows support is not guaranteed. JuliaBox is an online alternative that does not require any installation (see below).

Software installation

Please install these, prior to the workshop:

  • Julia. Scroll down to "Julia (command line version)", then download and run the installer that matches your system. If you need to install Julia from source, click on the "github" link, then scroll down for installation instructions.

    For most participants, the installer should work smoothly and fast. If this installer doesn't work and you need to install from source, compilation can take a while, so we strongly recommend that you install Julia prior to the workshop.

    To be able to run Julia from anywhere in a terminal, you need to add the julia executable to your path, or to have a link to it in a directory that is already in your path. For the first option on a Mac, you can open your bash profile (typically in ~/.bash_profile) and add this line: export PATH="$PATH:/Applications/Julia-0.6.3.app/Contents/Resources/julia/bin"

  • PhyloNetworks package (for network estimation). To install it, simply open Julia (open the app or type julia on the command line) and do this: Pkg.add("PhyloNetworks"). For plots, also install PhyloPlots with Pkg.add("PhyloPlots")

  • R (for TICR test)

  • R package phylolm which you can install from within R like this: install.packages("phylolm").

  • the TICR pipeline will be demonstrated, but there will not be enough time to run the full analysis of a large data set. Running it requires the prior installation of MrBayes, BUCKy, RAxML and Quartet MaxCut.

Julia Box

This website JuliaBox lets you run Julia within a browser: no set-up. It requires a browser only. Log in with any Google or GitHub account.

In the top main menu, click on "packages" to add PhyloNetworks and PhyloPlots (click on "Yours" and follow instructions). The upper right tab "New" will let you create folders, upload data, create a new IJulia notebooks etc. Your environment will be saved after you close your browser. Next time you log in with the same account, you will not need to add PhyloNetworks like the first time.


Can I bring and analyze my own data?

Definitely.

The upstream analyses can take a while, typically longer than the duration of the workshop (except for very few taxa), so we recommend that you run MrBayes + BUCKy or RAxML + ASTRAL prior to the workshop and bring their results, that is:

  • either a table of concordance factors and a first (rough) estimate of a species tree
  • or a list of gene trees, a first (rough) estimate of a species tree, and a list of files containing bootstrap trees, one for each gene.

See pages on this topic for scripts and detailed instructions to get there.

To analyze your data with PhyloNetworks during the timeframe of the workshop, we recommend less than 30 taxa. Tools for multiple alleles are available, but for now they have not been optimized (they're slow!) and not thouroughly tested yet (more on this in the next release!).

external links:

PhyloNetworks Workshop

Clone this wiki locally