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.
We finally have a page for the phylogenetic discussion group here in the department. It is here.
Giving the phyloseminar today.
Here are some instructions for the phylo seminar demos
get input files from here
get taxonomy from here
git clone https://github.com/OpenTreeOfLife/treemachine.git
git clone https://github.com/OpenTreeOfLife/gcmdr.git
git clone https://firstname.lastname@example.org/blackrim/avatol_nexsons.git
#DEMO 1 -- atol trees
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
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
#DEMO 3 -- birds
web site here http://files.opentreeoflife.org/
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
You can also get there here.
We recently had Celia Miller, a joint graduate student with Brad Cardinale, and Caroline Fukuchi, an undergrad, join the lab! Here are the lab folks.
next semester, I will be teaching a programming primer for graduate students. all the material will be at hackingtrees where there are materials also for the phylogenetics course. fun!
Along with Chris Dick at the University of Michigan and a number of other researchers at other institutions, we were awarded a grant to study the evolution of the andes. Here is the write up at U of Michigan.
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.
The lab just published a paper on some methods for combining trees in PLoS Comp Bio. You can get it here.
The construction of the draft tree of life with the Open Tree of Life project is still a work in progress. However, we have been working on ways of visualizing this draft tree and you can see some examples http://dev.opentreeoflife.org/ and you can see my favorite group with this link. Here is a different view with much more information.
Along with Gabriel Harp we have a Google summer of code student Chanda Phelan. She is part of the GNOME and NESCent summer of code allotment. She will be working on ways of visualizing phylogenies in graphs on the web and extending Phylet. Her progress is chronicled here.