| Robert Lanfear | Phyloworkshop

Schedule

May 24th: 0900-1000 Lecture: An introduction to phylogenetics (Simon Ho); 1000-1030 Lecture: Alignment in theory and practice (Rob Lanfear); 1030-1100 Questions and coffee; 1100-1200 Lecture: Model of molecular evolution, and how to select a good one (Rob Lanfear); 1200-1300 Lunch; 1300-1400 Practical: Xenoturbella and the diet of worms; 1400-1730 Practical: The evolution of whales and dolphins
May 25th: 0900-1000 Lecture: An introduction to Bayesian phylogenetics (Rob Lanfear); 1000-1100 Lecture: Bayesian phylogenetic analysis (Simon Ho); 1100-1130 Questions and coffee; 1130-1230 Lecture: Advanced Bayesian phylogenetic analysis (Simon Ho); 1230-1330 Lunch; 1330-1530 Practical: A mysterious hominin from Siberia; 1530-1730 Practical: The extinction of the cave bear

Software

Before coming to the workshop, please download and install the following software:

Geneious: Download link: http://www.geneious.com/; We'll use Geneious for alignments, basic phylogenetic analyses, and storing and annotating DNA sequences. You DO NOT need to buy a Geneious license for the workshop, just download the free trial version. All workshop attendees will be provided with an 8 week license for the pro version of Geneious. If you haven't had your email with the license key and you need one, email Rob. You'll also get a 25% discount if you choose to buy a full license after the workshop. None of the stuff you'll learn to do in the workshop is specific to Geneious - you can do all of it using free software if you choose. However, Geneious makes things a great deal easier, and a pro license is a worthwhile investment if you think you'll be dealing with a lot of DNA sequences in the future.
The PhyML plugin for Geneious: In Geneious, go to the "Geneious" item in the the top menu, then "Preferences". Select the "Plugins" tab, and select and install the PhyML plugin
PartitionFinder: Download link: http://www.robertlanfear.com/partitionfinder/; We'll use PartitionFinder to select partitioning schemes and models of molecular evolution.
Python: PartitionFinder also requires you to have Python. The PartitionFinder manual has detailed instructions on how to make sure you've got Python, so please read the manual carefully and make sure you have Python installed and working before you arrive at the workshop.
RaxML: Download link: http://sco.h-its.org/exelixis/software.html; We'll be using v7.0.3 for this workshop. On the download page, scroll down about 2/3 of the way to find the 'RaxML' section, then look for the section called 'Older Versions'. Alternatively, just search for this text in your browser: "RAxML v7.0.3". We'll be using RaxML to estimate phylogentic trees using Maximum Likelihood. v7.0.3 is not the most recent version, but it's the most recent one with downloadable executables for mac and windows. Everything we do will also work on the most recent versions of RaxML, so if you already have one of those versions, or would prefer to get one and know how to compile them from the source code, that's fine.
FigTree: Download link: http://tree.bio.ed.ac.uk/software/figtree/; FigTree is great for viewing and annotating pylogenetic trees. You can do much of the same stuff in Geneious, but Figtree is much better in many ways and can be used to make publication-ready figures.
Tracer: Download link: http://tree.bio.ed.ac.uk/software/tracer/; Tracer is great for visualising, analysing, and understanding the output from Bayesian MCMC runs.
BEAST: Download link: http://beast.bio.ed.ac.uk/; We'll use BEAST for all of the Bayesian phylogenetics and molecular dating on day two of the workshop.

ANU PhyloWorkshop

Schedule

May 24th

May 25th

Software

Geneious

The PhyML plugin for Geneious

PartitionFinder

Python

RaxML

FigTree

Tracer

BEAST

Location

Instructors

Participants