TreemixTutorial

TREEMIX

Program download: [ https://bitbucket.org/nygcresearch/treemix/wiki/Home goto the TREEMIX website]<br Tutorial material: download TREEMIX_TUTORIAL.ZIP

download the software as a tar.gz file is here: https://bitbucket.org/nygcresearch/treemix/downloads/treemix-1.12.tar.gz a git repository can be cloned like this: git clone https://bitbucket.org/nygcresearch/treemix.git

• unpack and/or cd into the folder: the treemix program needs additional libraries that are most likely not on your computer if you don't develop code. but try anyway first this:

./configure

if this breaks, check out what is missing: you may need to install the gnu scientific library: for example like this (the website is http://www.gnu.org/software/gsl/)

wget http://gnu.mirror.iweb.com/gsl/gsl-1.16.tar.gz then tar -xvfz gsl-1.16.tar.gz cd into gsl-1.16 read the README and INSTALL ./configure make make install # you may need sudo

if BOOST breaks then try this - figure out whether you have boost on your system, usually in /usr/local/boost - if not then install boost from here http://www.boost.org/build/ download a recent version for your system read: http://www.boost.org/doc/libs/1_55_0/doc/html/bbv2/installation.html

now try again you may need to do things like this

./configure --with-boost=/usr/local/boost --with-boostlib=/usr/local/boost/lib

Once all is installed, then read the manual in the treemix folder, the manual gives a short overview of the dataformat. See also our tutorial file example1.treemix.gz

commands to try are:

treemix -i example1.treemix -k 500 treemix -i example1.treemix -k 500 -o mytest -m 4

Once treemix has run, fire up R (I used R.app on my mac)

use (you will need to set the working path:

source("~/src/treemix/src/plotting_funcs.R")

plot_tree("mytest")

Explore what we can do with the output!