//Title of the output webpage
TITLE        = Nucleic data SPR benchmark
//Name of the output webpage file, completed with .html
RESULT FILE  = index
//Output directory, containing every output file
OUTPUT       = /auto/dufayard/LK_bench/revision/spr_n/
//Proteic data directory, must contain only valid input file for programs
NUCLEIC DATA = /auto/dufayard/dataset/Treebase/dataset2/nucleic_rough/
//Number of processor used on the cluster
PROCESSORS   = 1
//Minimum significant loglk difference
SIGNIFICANT PERCENTAGE = 25
RANKS
TOPOLOGY
RF

CLASS

PROGRAM PHYML_WIM
STORAGE = /auto/dufayard/LK_bench/revision/parc_wim/
TREE FILE = /auto/dufayard/LK_bench/revision/parc_wim/$INPUT_phyml_tree.txt
LK PATH = /auto/dufayard/LK_bench/revision/parc_wim_reopt/$INPUT_phyml_lk.txt
END;

PROGRAM PHYML_3.0_SPR_PARS=0
STORAGE = /auto/dufayard/LK_bench/revision/spr_nucl_0/
TREE FILE = /auto/dufayard/LK_bench/revision/spr_nucl_0/$INPUT_phyml_tree.txt
LK PATH = /auto/dufayard/LK_bench/revision/spr_nucl_0/$INPUT_phyml_lk.txt
END;

PROGRAM PHYML_3.0_SPR
STORAGE = /auto/dufayard/LK_bench/revision/spr_nucl/
TREE FILE = /auto/dufayard/LK_bench/revision/spr_nucl/$INPUT_phyml_tree.txt
LK PATH = /auto/dufayard/LK_bench/revision/spr_nucl/$INPUT_phyml_lk.txt
END;

PROGRAM PHYML_3.0_SPR_PARS=INFINITY
STORAGE = /auto/dufayard/LK_bench/revision/spr_nucl_infini/
TREE FILE = /auto/dufayard/LK_bench/revision/spr_nucl_infini/$INPUT_phyml_tree.txt
LK PATH = /auto/dufayard/LK_bench/revision/spr_nucl_infini/$INPUT_phyml_lk.txt
END;