The main SATé site is http://phylo.bio.ku.edu/software/sate/sate.html. This page just has information about the tutorial (first given the Washington DC Workshop on May 21, 2012).
The pdf version of the tutorial is at http://phylo.bio.ku.edu/software/sate/sate_tutorial.pdf it contains step by step instructions.
To run the command-line version on Mac, you'll need to:
shfollowed by the name of the setuptools egg
You can browse the issues for developers at https://github.com/sate-dev/sate-core/issues?state=open Many of these came from the morning in the workshop.
Please join SATé User Group for announcements about the software
For Derrick Zwickl's demo of GARLI and the DIMM model in GARLI, download http://phylo.bio.ku.edu/software/garli-SI.zip
Given the limited amount of time that we have to use GARLI today, the goal will be to get the program downloaded and do a quick set of runs with the gap models
Some general things to know about GARLI:
garli.conf. The program will look for this file in the current directory, but any filename can be passed on the command line.
To use the DIMM or Mkv gap models we first need to create a "gap coded" matrix that is just a direct copy of the DNA matrix with gaps as "0" and bases as "1". This is done with an external program called "gapcode". Scripts are provided to format nexus or fasta datasets for you, and to start the analyses. For the demo the dataset we'll use is called forTutorial.nex.
preparedDatadirectory. (These files are actually already there in the demo package, in case you have difficulty running gapcode.)
Now we run the DIMM and Mkv gap analyses by using other scripts:
|SATé user's group||http://groups.google.com/group/sate-user?hl=en|
|Other software for the demo|
|Java (if you don't have it)||http://www.java.com/en/|
|Installation for the command-line|
|Python (if you don't have it)||http://www.python.org/|
|wxPython (if *nix)||http://www.wxpython.org/|
|Other phylo (not needed for the demo)|
We gratefully acknowledge funding by the National Science Foundation grant (DEB-0732920 to Mark Holder) which supported the development of this software. See http://www.cs.utexas.edu/~tandy/ATOL-MSA.html for more information on this collaborative effort.