A bunch of procedures, common procs and APIs


Don Teng

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.

About This Repo

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 garauntee that each tutorial is entirely self-contained.

The tutorials in this repo will tend to contain information which is difficult to find, or is only the result of strenous research from poor documentation. Otherwise, I recommend Wikipedia articles or youtube videos for the basics - not (entirely) out of laziness, but because such content are made by people who make a living out of it, so they'll definitely be much better at teaching stuff, and their teaching material will be more highly polished.

These resources are loosely classified into themes, reflected in the title. For instance, we have a bunch of tutorials about the high-performance computing facility at Monash (M3), all prefixed with "m3", e.g. m3-quickstart, m3-about-the-hpc, and so on.

Things to Read up on

Mathematical Concepts

Recommended youtube channel: khan academy for undergrad-level theory, and mathematicalmonk for higher-level concepts. An in-depth knowledge of these concepts is not essential, unless you're aiming to specialize in that area - you certainly don't need to know how to do the maths by hand. An undergraduate understanding of these is sufficient; even Wikipedia is a little overkill.

  • Linear regression
  • Markov chains
  • Maximum likelihood
  • Bayesian statistics
  • MCMC - the most difficult of the lot. Don't bother if you don't need to know this.

Phylogenetics Concepts


Having a good grasp on how to read, if not write, code is helpful, but not essential.

  • Python, or R to start off. IMO, Python is superior to R in every way except for plotting. The Youtube channel thenewboston is a good place to start.
  • Github. Here's a recommended video.
  • Bash terminal, and Linux/Mac OS organization.

Software We Use

The following is a list of frequently-used-software. In general, try not to install computational software via ESS. The installation instructions shown here are only for Macs.

  • XCode and XCode Command Line Tools (for Macs) - sets up your Mac for development work. Get these first and foremost, because many of the computational programs require these to install properly.
  • homebrew - A Mac OS package manager. Get it here. You'll need XCode first, and maybe XCode CLT as well. Homebrew installs many kinds of software, including scientific software, into the directories of your Mac automatically so you don't have to organize all your software. For instance, to install software, use:
brew install my_software

To see if homebrew has your software available:

brew search my_software

Many of the computational programs are executables, so using homebrew will also save you having to mess with your $PATH and all that (if you don't know what that is, all the more reason to use homebrew!)

  • MAFFT - For multiple sequence alignment. An executable. Get it via homebrew.
  • RAxML - For computing trees using maximum likelihood. This is available on M3, so installing this is optional. Allegedly available via homebrew, but I never managed to get the homebrew-downloaded version working. In any case, it's so terribly slow that you may prefer to send all RAxML jobs to M3 anyway. In any case, here's my RAxML installation and quickstart tutorial, because it's probably the clunkiest software on this list - difficult to install and difficult to use.
  • IQ-Tree - For tree computation using maximum likelihood. An executable. Get it via homebrew.
  • FastTree - Fast tree computation. An executable. Get it via homebrew.
  • BEAST package - For tree computation using Bayesian statistics. Also has other secondary uses related to the understanding its own output, because the algorithms used to compute a Bayesian tree are not easy to understand. Version 1.8.4 is available here; that BEAST package also consists of accessory programs Tracer v1.6 and BEAGLE v2.1. Note that there's a version 2 available, though we're mostly still using version 1 so far.
  • FigTree - a nice, lightweight program for tree drawing. Simple installation.
  • TempEst - another nice program for tree drawing. We use it over FigTree because of one particular "find best root" function that's not available in FigTree.
  • CDhit - For clustering DNA sequences by similarity. An executable; get it via homebrew.
  • PAML - Multi-purpose analysis package with miscellaneous uses.
  • AliViewer - Allows you to look at a .fasta file of sequence data.

Unfortunately, almost all the software we use is not very well-documented, or the documentation is written in a way that's only accessible to intermediate users. This creates an odd catch-22 situation where beginners are kind of stranded without even being able to RTFM. In which case, it may take a bit of clever experimentation to figure out the software behaviour; there will also be tutorials available in this repo to walk you through it. An exchange between my old supervisor at VLSCI and I:

me : Doesn't anyone teach you how to use Bash?
jni: Nobody teaches you how to use Bash; you're just expected to know it.
me : Wait, then how did the first person learn to use Bash?
jni: That first person was the guy who created bash, so he didn't have to learn it!

For Python users:

  • Use Anaconda for automatic package management. Conda environments are also great for controlling your packages, and version control between Py36 and Py27.
  • Useful packages: pandas, numpy, Biopython, xlrd, scipy, scikit-bio
  • Jupyter recommended as an IDE.

Recommended Progression

Still thinking about this

  1. Get used to the Terminal: learn about homebrew. Get MAFFT and FastTree first. These are good starting points because they're fast and (relatively) easy. Other programs like RAxML and BEAST are more involved.
  2. Tree drawing with FigTree.

Other Recommended Reading