gistfile1.txt

[clustalw2]
args =
path = /panfs/pstor.storage/rcclocal/zcluster/pasta/1.6.3/bin/clustalw2

[commandline]
aligned = False
datatype = DNA
keepalignmenttemps = False
keeptemp = False
multilocus = False
raxml_search_after = False
two_phase = False
untrusted = False

[fakealigner]
path =

[faketree]
path =

[fasttree]
args =
model = -gamma -fastest
options =
path = /usr/local/fasttree/latest/FastTree

[hmmeralign]
path = /usr/local/pasta/latest/bin/hmmeralign

[mafft]
args =
path = /usr/local/mafft/latest/bin/mafft

[muscle]
args =
path = /usr/local/muscle/latest/bin/muscle

[opal]
args =
path = /panfs/pstor.storage/rcclocal/zcluster/opal/2.1.0/Opal.jar

[padaligner]
path =

[prank]
args =
path = /usr/local/prank/latest/prank

[probalign]
args =
path = /panfs/pstor.storage/rcclocal/zcluster/pasta/1.6.3/bin/probalign

[randtree]
path =

[raxml]
args =
model =
path = /usr/local/raxml/latest/raxmlHPC-MPI

[sate]
max_mem_mb = 10240
max_subproblem_frac = 0.25
merger = opal
num_cpus = 4