Phyloseminar notes

Giving the phyloseminar today.
Here are some instructions for the phylo seminar demos
get input files from here

get taxonomy from here

git clone
git clone
git clone

cd ../treemachine

#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
edit and to import your conf file

#DEMO 3 -- birds
cd ../treemachine

web site here

phylogenetic discussion and IRC

There are a small number of people that are exploring the old school tech way of discussion on the internet (IRC) for phylogenetics. You can find us on #phyloirc using the server. You can just click here
Visit the IRC channel

You can also get there here.

Looking for graduate students!

The Smith lab is looking for interested graduate students! If you want to work on plant evolution, evolution at a large scale, molecular evolution, computational and methodological phylogenetics, look no further! Send me an email and we can talk about projects, opportunities, and what it is like to be a graduate student here.

You can apply to the University of Michigan EEB program here and is the general department website.