maker_exe.ctl

#-----Location of Executables Used by MAKER/EVALUATOR
formatdb:/afs/nd.edu/user37/ccl/software/external/blast-2.2.16/bin/formatdb #location of NCBI formatdb executable
blastall:/afs/nd.edu/user37/ccl/software/external/blast-2.2.16/bin/blastall #location of NCBI blastall executable
#xdformat: #location of WUBLAST xdformat executable
#blastn:/afs/nd.edu/user37/biocmp/software/bin/blastn #location of WUBLAST blastn executable
#blastx:/afs/nd.edu/user37/biocmp/software/bin/blastx #location of WUBLAST blastx executable
#tblastx:/afs/nd.edu/user37/biocmp/software/bin/tblastx #location of WUBLAST tblastx executable
#xdformat: /afs/crc.nd.edu/user/a/athrash1/apps/bin/xdformat
#blastn: /afs/nd.edu/user28/dpandiar/emaker/external/exe/blast/bin
#blastx: /afs/nd.edu/user28/dpandiar/emaker/external/exe/blast/bin
#tblastx: /afs/nd.edu/user28/dpandiar/emaker/external/exe/blast/bin
RepeatMasker:/afs/nd.edu/user37/ccl/software/external/repeatmasker-3.2.8/RepeatMasker #location of RepeatMasker executable
exonerate:/afs/nd.edu/user37/ccl/software/external/exonerate-2.2.0/bin/exonerate #location of exonerate executable

#-----Ab-initio Gene Prediction Algorithms
snap:/afs/nd.edu/user37/ccl/software/external/snap-2009-12-04/bin/snap #location of snap executable
gmhmme3: #/afs/crc.nd.edu/user/a/athrash1/apps/gm_es_bp_linux64_v2.3d/gmhmme3 #location of eukaryotic genemark executable
gmhmmp: #location of prokaryotic genemark executable
augustus: #/afs/crc.nd.edu/user/a/athrash1/apps/augustus.2.5/bin/augustus #location of augustus executable
fgenesh: #location of fgenesh executable
twinscan: #location of twinscan executable (not yet implemented)

#-----Other Algorithms
jigsaw: #location of jigsaw executable (not yet implemented)
qrna: #location of qrna executable (not yet implemented)
fathom: #location of fathom executable (not yet implemented)
probuild: #/afs/crc.nd.edu/user/a/athrash1/apps/gm_es_bp_linux64_v2.3d/probuild#location of probuild executable (required for genemark)