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caseywdunn /
Last active August 29, 2015 13:57
Agalma installation scripts
# This is a full set of commands to install [Agalma](
# from the on Ubuntu Server from the tarballs. It has been tested on the AWS Ubuntu Server AMI.
sudo apt-get update
sudo apt-get install make
sudo sh
caseywdunn / TREE_tree.tre
Created May 14, 2015 02:38
Newick representation of the phylogenetic tree in Figure 1 of our TREE review on animal phylogenetics (
caseywdunn /
Last active October 30, 2016 20:08
Notes from my October 7, 2016 talk at the Boston Evolutionary Genomics Supergroup Meeting
caseywdunn /
Last active September 25, 2017 18:22
Regular expressions intro and examples

Working with Conda

First, some nomenclature (see for more):

  • A recipe is a flat directory that has the information needed to build a package
  • A package is a "compressed file that contains everything that a software program needs in order to be installed and run... You manage conda packages with conda."
  • An environment is a "directory that contains a specific collection of conda packages and their dependencies, so they can be maintained and run separately without interference from each other."

A typical workflow:

caseywdunn /
Last active March 5, 2018 22:36
Notes to accompany my talk.

Evolution 2017

June 25, 2017 (and updated since then)

Casey Dunn, , @caseywdunn

These are some notes and annotated references relevant to my talk with Stacey Smith in the symposium "SSB Symposium Phylogenetic approaches to connecting genotypes to phenotypes" at Evolution 2017.

If you are interested in any of this work let me know. I am moving to Yale and looking for people to join the new research group.

caseywdunn /
Last active May 21, 2018 17:27
Postdoc position: HIV phylogenetics in the Dunn Lab at Yale University
caseywdunn /
Created June 24, 2016 18:17
Setup and examples of virtualenv on osx
# Setting up virtualenv on macOS Yosemite
brew update
brew upgrade
which python # check location of system version
brew install python
brew install freetype # Needed by some python packages
brew install libxml2 # Needed by some python packages
pip install virtualenv virtualenvwrapper pytest