catabolism 53 53 optimizeGeneTrees ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_catabolism_results/results/catabolism/geneTree.newick ../Histamine_system/Analysis/ufb_reconciliation_inputFiles/mapping_file_catabolism.txt ../Histamine_system/Analysis/after_tindex_LSI/catabolism.fasta ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_catabolism_results/species_trees/inferred_species_tree.newick WAG+F+I+G4 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_catabolism_results/gene_optimization_3/dtl_rates.txt 0 0 1 UNIFORM 0 1 0 0 PARENTS 0 0 0.000001 NONE 0 2 -1 1 1 1 4 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_catabolism_results/results/catabolism/geneTree.newick ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_catabolism_results/results/catabolism/stats.txt 0 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_catabolism_results/gene_optimization_3/checkpoints/catabolism
