-message "Check tree cost 1 chromosome ua.poy" -command "ua.poy" -cost 208 
-message "Check tree cost ua2 with locus_indel chromosome ua2.poy" -command "ua2.poy" -cost 482
-message "Check tree cost ua3 with min_rearrangement_len chromosome ua3.poy" -command "ua3.poy" -cost 208
-message "Check tree cost ua4 with min_loci_len chromosome ua4.poy" -command "ua4.poy" -cost 208
-message "Check tree cost an2 with locus_indel annotated chromosome an2.poy" -command "an2.poy" -cost 40 
-message "Check tree cost an3 with min_rearrangement_len annotated chromosome an3.poy" -command "an3.poy" -cost 40
-message "Check tree cost FILENAME1 cnc.poy" -command "cnc.poy" -inputfile first_fasta -costfile cnc.costs
-message "Check tree cost FILENAME1 cnc1.poy" -command "cnc1.poy" -costfile cnc1.costs -inputfile first_fasta
-message "Check tree cost FILENAME1 cnc2.poy" -command "cnc2.poy" -costfile cnc2.costs -inputfile first_fasta
-message "Check tree cost FILENAME1 cnc3.poy" -command "cnc3.poy" -costfile cnc3.costs -inputfile first_fasta
-message "Check tree cost FILENAME1 cc.poy" -command "cc.poy" -costfile cc.costs -inputfile first_fasta
-message "Check tree cost FILENAME1 cc1.poy" -command "cc1.poy" -costfile cc1.costs -inputfile first_fasta
-message "Check tree cost FILENAME1 cc2.poy" -command "cc2.poy" -costfile cc2.costs -inputfile first_fasta
-message "Check tree cost FILENAME1 cc3.poy" -command "cc3.poy" -costfile cc3.costs -inputfile first_fasta
-message "Check tree cost after static approx FILENAME1 sa.poy" -command "sa.poy" -costfile sa.costs -inputfile first_fasta
-message "Check tree cost after static approx FILENAME1 sa1.poy" -command "sa1.poy" -costlessfile sa1.costs -inputfile first_fasta
-message "Check tree cost with static and polymorphisms static_poly.poy" -command "static_poly.poy" -cost 1298 
