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

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