From Lab to the World

Course materials for Michael Dunn's course at the 2018 LOT Winter School

Lecture outline and readings

Software requirements

Exercise 1: Bayesian Phylogenetic Inference with MrBayes
Datafile: Aslian28.nex

Exercise 2: Constraints and multiple partitions
Datafiles: new-britain-swadesh.nex, new-britain-structural.nex

Exercise 3: Ancestral State Reconstruction and the DISCRETE test
Datafiles: Aslian28+structure1.nex, Aslian28.nex.trees, Aslian-complexity.txt, Aslian-semantics.txt

Crash course in commandline computing

The software carpentry version of this is nice to read:

Windows computers have something called “Powershell”. According to the wikipedia documentation, all the basic unix commands are aliases to equivalent Powershell commands, so the following instructions should work on Windows too (although I wouldn’t expect the option flags to be the same).

The description below is stolen from http://mally.stanford.edu/~sr/computing/basic-unix.html. I’ve chopped out the bits I don’t think you need, and added a couple of other things. Things written like this are what you should type into the Terminal window. Things in ALL CAPS should be substituted for actual file/directory names, etc. Unix commands are all case-sensitive: myFile.txt is not the same things as MYFILE.txt or myfile.TXT, etc.

Directories (also called “folders” on a Macintosh), are used to group files together in a hierarchical structure. These are the same directories you can see using the MaxOSX Finder.

Files

Convenience

Inconvenience