This first introductory page contains a bunch of essential readings to get the basics first. Useful sources: Wikipedia, Reddit Explain Like I'm 5 (ELI5), Khan Academy (for undergraduate-level academic concepts), Stackoverflow (a Q&A site for programming), Youtube.
This repo contains several tutorial files, with varying levels of difficulty. Recommended prerequisites will be listed near the top of that tutorial. 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.
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
Software for tree reconstruction- 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.
Using high-performance computers
data-wrangling] - Upcoming. Some recommended practices for virus name configurations, what kind of files to prepare, and how to pass data to your RA.
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.
things-to-read-up-on- Don's things to read up on.
London BEAST workshop notes- Don's notes from London.