catabolism 53 53 optimizeGeneTrees /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_catabolism_results/results/catabolism/geneTree.newick ../Histamine_system/Analysis/tbe_reconciliation_inputFiles/mapping_file_catabolism.txt ../Histamine_system/Analysis/after_tindex_LSI/catabolism.fasta /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_catabolism_results/species_trees/inferred_species_tree.newick WAG+F+I+G4 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_catabolism_results/gene_optimization_4/dtl_rates.txt 0 0 1 UNIFORM 0 1 0 0 PARENTS 0 0 0.000001 NONE 0 2 -1 1 1 1 5 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_catabolism_results/results/catabolism/geneTree.newick /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_catabolism_results/results/catabolism/stats.txt 0 /mnt/myhdd/ankit/Histamine_system/Analysis/tbe_reconciliation_OUT_OTOL_NEW/familyfile_catabolism_results/gene_optimization_4/checkpoints/catabolism
