vjlab/resources

Commonly used phylogenetic methods, Monash HPC access and basic bioinformatics

Introduction

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Don Teng

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.

1. Lab Admin

• data storage facilities - Data storage and archiving facilities available.

2. Theory and Software

• Commonly used file formats - Tutorial on commonly used file formats like fasta, phy, etc.
• 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, treesub.
• 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.

3. 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.

4. Tech Tips

• 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 pandas library.
• 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.