//Title of the output webpage
TITLE        = Proteic 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/proteic_cat/
//Proteic data directory, must contain only valid input file for programs
PROTEIC DATA = /auto/dufayard/dataset/Treebase/dataset2/proteic_rough/
//Number of processor used on the cluster
PROCESSORS   = 1
//Minimum significant loglk difference
SIGNIFICANT PERCENTAGE = 25
RANKS
TOPOLOGY
RF

CLASS

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

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

PROGRAM RAXML_CAT
STORAGE = /auto/dufayard/LK_bench/revision/raxml_cat_prot_reopt/
TREE FILE = /auto/dufayard/LK_bench/revision/raxml_cat_prot/RAxML_result.$INPUT_RAXML_CAT
LK PATH = /auto/dufayard/LK_bench/revision/raxml_cat_prot_reopt/$INPUT_phyml_lk.txt
END;

PROGRAM FAST_TREE
STORAGE = /auto/dufayard/LK_bench/revision/fasttree_proteic_reopt/
TREE FILE = /auto/dufayard/LK_bench/revision/fasttree_proteic/$INPUT_FAST_TREE
LK PATH = /auto/dufayard/LK_bench/revision/fasttree_proteic_reopt/$INPUT_phyml_lk.txt
END;