Lab of Stephen A. Smith

01/11/2009

About

I am Stephen A. Smith, an evolutionary biologist and Assistant Professor at the University of Michigan, Ann Arbor. You can find out more information about the people in the lab here and the projects here. A lot of the research in the lab focuses on plant evolution, detecting and describing large scale patterns of evolution, examining differences in the rate of molecular evolution, and using new data sources like transcriptomes and genomes to address these questions. A great deal of this involves the development of new methods and new computational tools. My faculty page is here.

02/13/2014

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/

01/28/2014

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 freenode.net server. You can just click here
Visit the IRC channel

You can also get there here.