biosynthesis 149 149 optimizeGeneTrees ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_biosynthesis_results/results/biosynthesis/geneTree.newick ../Histamine_system/Analysis/ufb_reconciliation_inputFiles/mapping_file_biosynthesis.txt ../Histamine_system/Analysis/after_tindex_LSI/biosynthesis.fasta ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_biosynthesis_results/species_trees/inferred_species_tree.newick LG+R7 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_biosynthesis_results/gene_optimization_2/dtl_rates.txt 0 0 1 UNIFORM 0 1 0 0 PARENTS 0 0 0.000001 NONE 0 2 -1 1 1 1 3 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_biosynthesis_results/results/biosynthesis/geneTree.newick ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_biosynthesis_results/results/biosynthesis/stats.txt 0 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_biosynthesis_results/gene_optimization_2/checkpoints/biosynthesis
