# SATe configuration file.  Feed it to 'run_sate.py' with the '-c' flag:
# run_sate.py -c sate.cfg <other stuff>
# NOTE that sate will currently run only on the CLAW nodes (claw1-claw4)
# and /or only in the SGE 'claws' Queue


# comments in this file MUST start in the 1st column with a '#'
# all other comment formats will fail.

# this is an example of an allowed comment. It can remain
         # this BAD COMMENT line will cause failure.  remove it before trying it
[clustalw2]
path = /usr/bin/clustalw2

[mafft]
path = /usr/local/bin/mafft    # another BAD COMMENT 

[muscle]
path = /usr/bin/muscle    ; still another BAD COMMENT.

[opal]
path = /usr/local/bin/opal.jar

; also a BAD COMMENT; has to begin with a '#', not a ';'
[prank]
path = /usr/local/bin/prank

[raxml]
path = /usr/local/bin/raxmlHPC

[sate]
time_limit = 86400
max_subproblem_size = 0.2
aligner = mafft
merger = muscle
tree_estimator = raxml
num_cpus = 2
break_strategy = centroid