//Title of the output webpage
TITLE        = Simulated data 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/simu/
//Proteic data directory, must contain only valid input file for programs
NUCLEIC DATA = /auto/dufayard/dataset/simulated_phyml/alignments/
//Number of processor used on the cluster
PROCESSORS   = 1
//Minimum significant loglk difference
SIGNIFICANT PERCENTAGE = 25
RANKS
TOPOLOGY
TRUE TREES = /auto/dufayard/dataset/simulated_phyml/truetrees/$INPUT_truetree.txt
RF

CLASS

PROGRAM PHYML_2.4.5
STORAGE = /auto/dufayard/LK_bench/simu_2.4.5/
TREE FILE = /auto/dufayard/LK_bench/simu_2.4.5/$INPUT_phyml_tree.txt
LK PATH = /auto/dufayard/LK_bench/simu_2.4.5_reopt/$INPUT_phyml_lk.txt
END;

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

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

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

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

PROGRAM RAXML
STORAGE = /auto/dufayard/LK_bench/simu_raxml/
TREE FILE = ../simu_raxml/RAxML_result.$INPUT_RAXML
LK PATH = /auto/dufayard/LK_bench/simu_raxml_reopt/$INPUT_phyml_lk.txt
END;