
A very short guide to using non-graphical versions of GARLI:

1. Move or copy the GARLI executable (in the bin directory
 for precompiled versions) into the same directory as a
 GARLI configuration file named garli.conf and a dataset to 
 be analyzed (in Nexus, Pylip or Fasta format).

2. Edit the garli.conf file in a text editor and enter the
 name of the dataset to be analyzed on the datafname line.
 The other lines in the configuration file can be ignored 
 for now.

3. On Windows you can then double-click the executable.  On
 other OS's you will need to start the program from the command
 line.  In a terminal window, get to the directory with the
 files in it.  Start the program with 
 ./GarliXXX
 where the XXX will depend on the exact version of the program.

4. Look through the output files that have been created.  They
 contain a variety of information about the search itself as well
 as the details of the inferred tree and model of substition.

To try it out on the included sample dataset, just copy the 
program and execute it from the example/basic/ directory,
without needing any other setup. This reads the garli.conf 
file in that directory, which is set up to analyze the 
included 64 taxon rana.nex dataset (this should take between
10 and 30 minutes, depending on the speed of your computer).

You can also find sample configuration files that you can alter
for your data in the example/basic directory.

Configuration of partitioned models is necessarily more complex,
but examples and template configuration files appear in the
example/partition directory.  See the support wiki listed below
for lots more information.

You can specify configuration files to use that are not named
garli.conf by passing them on the command line:
./GarliXXX myconfigurationfilename

To avoid having to copy the executable into each run directory
you can either put it somewhere in your path (OS X or linux),
make a shortcut in the directory (Windows) or make a symbolic
to the executable in the directory (OS X or linux)

For further details, see the GARLI Manual or visit the Garli
Wiki support webpage: http://www.nescent.org/wg/garli

Have fun, and let me know of any questions, problems or feedback:
Derrick Zwickl
garli.support@gmail.com

