-message "Check custom alphabet read" -command "ca.poy"
-message "Check custom alphabet ia" -command "ca1.poy"
-message "Check ia for chromosome" -command "ua1.poy"
-message "Check tree build for annotated chromosome an.poy" -command "an.poy" 
-message "Check ia for annotated chromosome an1.poy" -command "an1.poy"
-message "Check transform with min_loci_len annotated chromosome an4.poy" -command "an4.poy" -stderr "an4.poy.err"
-message "Check transformation into static sankoff character sk.poy" -command "sk.poy"
-message "Check break inv read" -command "bi.poy" -stderr "bi.poy.err"
-message "Check break inv ia" -command "bi1.poy" -stderr "bi1.poy.err"
-message "Check xml output bi2.poy" -command "bi2.poy"  -stderr "bi2.poy.err"
-message "Check xml output ca3.poy" -command "ca3.poy"
-message "Check xml output an5.poy" -command "an5.poy" 
-message "Check xml output of sankoff character sk1.poy" -command "sk1.poy" 
-message "Check xml output for chromosome ua5.poy" -command "ua5.poy"
-message "Check build and search FILENAME1 bs.poy" -command "bs.poy" -inputfile all_fasta
-message "Check build and search FILENAME1 bs1.poy" -command "bs1.poy" -inputfile all_fasta
-message "Check build and search FILENAME1 bs2.poy" -command "bs2.poy" -inputfile all_fasta
-message "Check build and search FILENAME1 bs3.poy" -command "bs3.poy" -inputfile all_fasta
-message "Check build and search FILENAME1 bsa.poy" -command "bsa.poy" -inputfile all_fasta
-message "Check build and search FILENAME1 bs1a.poy" -command "bs1a.poy" -inputfile all_fasta
-message "Check build and search FILENAME1 bs2a.poy" -command "bs2a.poy" -inputfile all_fasta
-message "Check build and search FILENAME1 bs3a.poy" -command "bs3a.poy" -inputfile all_fasta
-message "Check auto sequence partition FILENAME1 asp.poy" -command "asp.poy" -inputfile all_fasta
-message "Check auto static approx FILENAME1 asx.poy" -command "asx.poy" -inputfile all_fasta
-message "Check static homology characters after converting from sequences FILENAME1 sh1.poy" -command "sh1.poy" -inputfile first_fasta