Happy to add Drew Larson and Lijun Zhao to the lab! Drew is co-advised with Chris Dick in the department.
Ya Yang has been a member of the lab working on transcriptomics in Caryophyllales and will be moving on to a position at UMinn this fall. Congrats Ya! http://www.yangya.org/
James Pease has been a member of the lab working on the Andes and got a position at Wake Forest. Congrats! https://peaselab.github.io/
Two new postdocs will be joining the lab. More on that in a bit
There is code that implements most of what we go over 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/
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 lab just published a paper on some methods for combining trees in PLoS Comp Bio. You can get it here.
Just got back from teaching at the Computational Molecular Evolution course . Was good fun and saw some great lectures. B. Moore took this with Ben Redelings, Tracey Heath and myself in front of Trinity College.
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
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).