This is a collection of files used to demonstrate the use of a phylogenetic placement-based workflow. It can be used on the linux or OS X platforms, and for windows users it works great on the QIIME virtual box. A reasonably recent laptop with 2GB of memory should be able to run this code just fine if you don't have too many other things open.
This demo can be downloaded
here.
You will need to download the v1.1 pplacer suite as well.
There is a download.sh script in the bin directory which
will get it, or you can visit the
pplacer website.
You will then need to put pplacer, guppy, and rppr in your path.
SQLite3 is only necessary for one part of the demo. It is already installed on recent OS X macs. If you want to install it on an Debian/Ubuntu system (e.g. the QIIME virtual box) just run an
sudo apt-get install sqlite3
QIIME users: the password is qiime.
Simply execute the script pplacer_demo.sh. This script was meant to be read,
and pplacer_demo.html is a marked
up version of it.
Noah Hoffman, Aaron Gallagher and Erick Matsen.
The data for this demonstration was generated as part of ongoing work at the Fred Hutchinson Cancer Research Center on the microbiome of the vagina. We would like to thank Martin Morgan, Sujatha Srinivasan and David Fredricks for their work and for allowing the data to be used.