Lab of Stephen A. Smith



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.


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.