transport 494 494 optimizeGeneTrees ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_transport_results/results/transport/geneTree.newick ../Histamine_system/Analysis/ufb_reconciliation_inputFiles/mapping_file_transport.txt ../Histamine_system/Analysis/after_tindex_LSI/transport.fasta ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_transport_results/species_trees/inferred_species_tree.newick LG+F+R9 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_transport_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 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_transport_results/results/transport/geneTree.newick ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_transport_results/results/transport/stats.txt 0 ../Histamine_system/Analysis/ufb_reconciliationOUT_opeTreeofLife/familyfile_transport_results/gene_optimization_4/checkpoints/transport
