This is a collection of get started pages and introductory tutorials for computational methods routinely used within the group, followed by details on access to high-performance computing access within Monash, and links to bioinformatics beginners tutorials. Recommended prerequisites are listed at the top of that page. However, try as I might to make them so, there's no guarantee that each tutorial is entirely self-contained, but the idea is that you should be able to start anywhere.
- data storage facilities - Data storage and archiving facilities available.
Theory and Software
Commonly used file formats- Tutorial on commonly used file formats like
Multiple sequence alignment - introduction- How to do multiple sequence alignment, part 1
Multiple sequence alignment using MAFFT- How to do multiple sequence alignment (using
mafft), part 2
Tree computation part 1: theory- A not-so-brief introduction to ML trees and BEAST trees.
Tree computation part 2: software- How to use various programs to compute a tree, and their pros and cons
BEAST tutorial links- A link to existing BEAST tutorials.
PAML-TREESUB- How to install and use
PAML, and an associated program,
RAxML- How to install RAXML, and basic usage.
- Selection analysis with
HyPhy- quickstart tutorial.
MrBayes Quickstart- Getting started with MrBayes, for Bayesian MCMC tree computation.
Using high-performance computers
hpc-resources- A quick overview of the HPC and data-serving resources available, and basic usage policies.
about-our-hpc- How to use the lab's internal server, located in room 217
m3-quickstart- A tutorial on how to send a job to M3.
m3-tips-and-tricks- A dumping ground for how to use M3 slightly more efficiently.
Software installation and prep work- Software we used, and some basics to read up on.
Data wrangling with python- Data wrangling with python, using the
R-ggtree-demo- How to plot some basic trees with
ggtree, in R. This PDF document should be viewable in your browser, but doesn't always; you can download it to view it if required.
misc-learning-to-code- tutorial on how to learn to code, not actually on how to code. Has links for the latter.
software-python-resources- A bunch of python resources.
software-tips-and-tricks- A dumping ground for miscellaneous bash or computational tips and tricks.
tech-github- Tutorial for basic command line usage of Github.
misc-writing- How to write so that others can understand you.
London BEAST workshop notes- Don's notes from London.