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.
Caroline Parins-Fukuchi has decided to join the lab as a graduate student!
We have gotten the first data out from our Caryophyllales grant (together with 1KP data). We discuss gene and genome duplication, rates of molecular evolution and other fun things!
Yang, Y. M.J. Moore, S.F. Brockington, D.E. Soltis, G.K.-S. Wong, E.J. Carpenter, Y. Zhang, L. Chen, Z.-X. Yan, Y.-L. Xie, R.F. Sage, S. Covshoff, J.M. Hibberd, M.N. Nelson, and S.A. Smith. Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing. Molecular Biology and Evolution.
With the support of the Caryophyllales grant, we have published (Sam Brockington and Ya Yang as co-first authors).
Brockington S.F., Y. Yang, F. Gandia-Herrero, S. Covshoff, J.M. Hibberd, R.F. Sage, G.K.-S. Wong, M.J. Moore and S.A. Smith. Lineage specific gene radiations underly the evolution of novel betalain pigmentation in Caryophyllales. New Phytologist.
We posted a bioarxiv version of our OpenTree paper that is in review here. Fun!
There is code that implements most of what we go over here.
Ya Yang and Smith published a paper in MBE on orthology methods and phylogenomics. Check it here.
Cody and Stephen published a paper on the limitations of public data to construct large phylogenetic trees. Check it out 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://email@example.com/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.