Phyloseminar notes

Giving the phyloseminar today.
Here are some instructions for the phylo seminar demos
get input files from here
http://blackrim.org/datafiles/phylo_seminar_files2014.tar.gz

get taxonomy from here
http://files.opentreeoflife.org/ott/

git clone https://github.com/OpenTreeOfLife/treemachine.git
git clone https://github.com/OpenTreeOfLife/gcmdr.git
git clone https://blackrim@bitbucket.org/blackrim/avatol_nexsons.git

cd ../treemachine
./mvn_cmdline.sh

#DEMO 1 -- atol trees
cd treemachine
java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar justtrees atol/RAxML_bootstrap.WITH_MT_BS100.rr T life atol.db
java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar graphml life atol.graphml F atol.db

#DEMO 2 -- tree + taxonomy
cd ../gcmdr
edit config file (the demo one is called stephen_laptop_conf.py)
edit load_taxonomy.py and synth_one_study.py to import your conf file
python load_taxonomy.py
python synth_one_study.py

#DEMO 3 -- birds
cd ../treemachine
bash DEMO_run_birds_example.sh

#DEMO 4
web site here http://files.opentreeoflife.org/

Hackingtrees.net

I have launched a new page for my class EEB 491 in phylogenetic methods and theory. It will have code and algorithms for many of the procedures and will continue to grow. It is for the class, but anyone can comment, or contribute.

You can see it here hackingtrees.net

Graduate students

University of Michigan is currently accepting graduate students (see link here) and I am always looking for good students interesting in computational molecular evolution, large scale plant evolution, biogeography, and phylogenetics. If you are interested in joining the lab, check out some recent publications and drop me an email. Here is my faculty page for my email (don’t want to post it here for spam).