-command accessory/cd_pwd01.poy -message "'cd' and 'pwd' stderr" 
-command accessory/clear_memory01.poy -message "'clear_memory' under defaults"
-command accessory/clear_memory02.poy -message "'clear_memory' with all arguments"
-command accessory/echo01.poy -message "'echo' stderr outputs, verify by stderr" -stderr "accessory/stderr/echo01.poy.stderr" -error
-command accessory/echo02.poy -message "'echo' text output" 
-command accessory/echo03.poy -message "'echo' stdout outputs, verify by stdout" -stdout "accessory/stdout/echo03.poy.out"
-command accessory/echo04.poy -message "'echo' stderr outputs, verify by stderr" -stderr "accessory/stderr/echo04.poy.err" -error
-command accessory/exit01.poy -message "'exit' with arguments; ERROR expected" -stderr "accessory/stderr/exit01.poy.err" -error
-command accessory/exit02.poy -message "'exit', just checking if works"
-command accessory/help01.poy -message "confirming 'help' is working"
-command accessory/quit01.poy -message "'quit' with arguments, ERROR expected" -stderr "accessory/stderr/quit01.poy.err" -error
-command accessory/quit02.poy -message "'quit', just checking if works"
-command accessory/rediagnose.poy -message "'rediagnose' test" -stderr "accessory/stderr/rediagnose.poy.err"
-command accessory/redraw01.poy -message "'redraw', just checking if works"
-command accessory/redraw02.poy -message "'redraw' with specified argument, ERROR expected" -stderr "accessory/stderr/redraw02.poy.err" -error
-command accessory/rename01.poy -message "'rename' with synonymy file" -stdout "accessory/stdout/rename01.poy.out"
-command accessory/rename02.poy -message "'rename' specifying a pair of synonyms" -stdout "accessory/stdout/rename02.poy.out"
-command accessory/run01.poy -message "'run' without argument, ERROR expected" -stderr "accessory/stderr/run01.poy.err" -error
-command accessory/run02.poy -message "'run' using multiple scripts" -stderr "accessory/stderr/run02.poy.err" -stdout "accessory/stderr/run02.poy.out" -error
-command accessory/version01.poy -message "'version' test"
-command accessory/wipe01.poy -message "'wipe'; just to see if works 1"
-command accessory/wipe02.poy -message "'wipe'; just to see if works 2"
-command accessory/wipe03.poy -message "'wipe' with argument, ERROR expected" -stderr "accessory/stderr/wipe03.poy.err" -error
-command build/build.poy -message "build using default settings with fasta, ss, and aa files build.poy " -stderr "build/stderr/build.poy.err"
-command build/build1.poy -message "build 1 tree with fasta, ss, and aa files build1.poy" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "build/stderr/FILENAME1_FILENAME2_FILENAME3.build1.poy.err"
-command build/build10.poy -message "build with all with fasta, ss, and aa files with random build10.poy" -inputfile "fas" -inputfile "ss" -inputfile "aa"
-command build/build11.poy -message "build with all with fasta, ss, and aa files with randomized build11.poy" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "build/stderr/FILENAME1_FILENAME2_FILENAME3.build11.poy.err"
-command build/build12.poy -message "build under iterative exact build12.poy" -stderr "build/stderr/build12.poy.err"
-command build/build2.poy -message "build as_is with fasta, ss, and aa files build2.poy" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "build/stderr/FILENAME1_FILENAME2_FILENAME3.build2.poy.err"
-command build/build3.poy -message "build 3 trees with fasta, ss, and aa files build3.poy" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "build/stderr/FILENAME1_FILENAME2_FILENAME3.build3.poy.err"
-command build/build4.poy -message "build with 1.fas specifying a negative number Expect Error build4.poy" -stderr "./build/stderr/build4.err" -error
-command build/build5.poy -message "build with all with fasta, ss, and aa files build5.poy" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "build/stderr/FILENAME1_FILENAME2_FILENAME3.build5.poy.err"
-command build/build6.poy -message "build with of_file with fasta file 2.fas, read tree 2.fas.2.tree build6.poy" -stderr "build/stderr/build6.poy.err"
-command build/build7.poy -message "build for xml.output build7.poy" -stderr "build/stderr/build7.poy.err"
-command build/build8.poy -message "build with all with fasta, ss, and aa files branch and bound build8.poy" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stdout "build/stdout/FILENAME1_FILENAME2_FILENAME3.build8.poy.out"
-command build/build9.poy -message "build with all with fasta files with constraint build9.poy" -stderr "build/stderr/build9.poy.err"
-command fuse/fuse.poy -message "test build 2 trees and default fuse with fasta and ss files fuse.poy" 
-command fuse/fuse.poy -message "test build 2 trees and default fuse with fasta and ss files fuse.poy" -stderr "./fuse/stderr/fuse.poy.err"
-command fuse/fuse1.poy -message "test build 3 trees and fuse keep 2 for with fasta and ss files fuse1.poy" 
-command fuse/fuse1.poy -message "test build 3 trees and fuse keep 2 for with fasta and ss files fuse1.poy" -stderr "./fuse/stderr/fuse1.poy.err"
-command fuse/fuse11.poy -message "test fuse swap with constraint with fasta and ss files" 
-command fuse/fuse12.poy -message "test fuse swap with swap around with fasta and ss files" 
-command fuse/fuse13.poy -message "test fuse with swap tbr with fasta and ss files" 
-command fuse/fuse14.poy -message "test fuse with swap threshold 5 with fasta and ss files" 
-command fuse/fuse2.poy -message "Fuse with 1.fas fasta files without build, Expect Error There are no active trees in memory fuse2.poy" -stderr "./fuse/stderr/fuse2.poy.err" -error
-command fuse/fuse3.poy -message "Fuse from read tree files without data file Expext error could not find data fuse3.poy" -stderr "./fuse/stderr/fuse3.poy.err" -error
-command fuse/fuse4.poy -message "test build, fuse from read tree files with fasta file 2.fas.1.tree fuse4.poy" 
-command fuse/fuse5.poy -message "test build and fuse with 10 iterations with fasta ss files fuse5.poy"
-command fuse/fuse6.poy -error -message "Fuse with fasta and ss files with a float rather than an integer for iterations, Expect Error" 
-command fuse/fuse7.poy -message "Fuse with fasta and ss files with a float rather than an integer for keep, Expect Error" -stderr "./fuse/stderr/fuse7.err" -error
-command fuse/fuse8.poy -message "test fuse with better with fasta and ss files fuse8.poy"
-command fuse/fuse9.poy -message "test build and fuse with 10 iterations with fasta and ss files fuse9.poy" 
-command perturb/perturb02.poy -message "'perturb' defaults, no builds, wmessages expected" -stderr "perturb/stderr/perturb02.poy.err" -error
-command perturb/perturb03.poy -message "default 'perturb' with 'build' and default 'swap' for for fas, ss, and aa data" -stderr "perturb/stderr/perturb03.poy.err"
-command perturb/perturb04.poy -message "'perturb' with integer argument and 'build'; ERROR expected" -stderr "perturb/stderr/perturb04.poy.err" -error
-command perturb/perturb05.poy -message "'perturb' with specified iterations and 'build' for fas, ss, and aa data" -stderr "perturb/stderr/perturb05.poy.err"
-command perturb/perturb06.poy -message "'perturb' with negative number of iterations; ERROR expected" -stderr "perturb/stderr/perturb06.poy.err" -error
-command perturb/perturb07.poy -message "'perturb' with decimal number of iterations; ERROR expected" -stderr "perturb/stderr/perturb07.poy.err" -error
-command perturb/perturb08.poy -message "'perturb' with default 'ratchet' for fas, ss, and aa data" -stderr "perturb/stderr/perturb08.poy.err"
-command perturb/perturb09.poy -message "'perturb' with default 'ratchet'; ERROR expected" -stderr "perturb/stderr/perturb09.poy.err" -error
-command perturb/perturb10.poy -message "default 'perturb' with 'build' and 'swap' under 'static_approx' using fas and aa" 
-command perturb/perturb11.poy -message "default 'perturb' with 'build' and multiple 'swap' arguments for fas, ss, aa" -stderr "perturb/stderr/perturb11.poy.err"
-command perturb/perturb12.poy -message "'perturb' using 'ratchet' with specified values for fas, ss, aa" -stderr "perturb/stderr/perturb12.poy.err"
-command perturb/perturb13.poy -message "'perturb' using 'ratchet' with reversed order of float and integer values; ERROR expected" -stderr "perturb/stderr/perturb13.poy.err" -error
-command perturb/perturb14.poy -message "'perturb' using 'ratchet' with integer values; ERROR detected" -stderr "perturb/stderr/perturb14.poy.err" -error
-command perturb/perturb15.poy -message "'perturb' using 'ratchet' with float values, ERROR expected" -stderr "perturb/stderr/perturb15.poy.err" -error
-command perturb/perturb16.poy -message "'perturb' using 'ratchet' with negative float value, ERROR expected" -stderr "perturb/stderr/perturb16.poy.err" -error
-command perturb/perturb17.poy -message "'perturb' using 'ratchet' with negative integer value, ERROR expected" -stderr "perturb/stderr/perturb17.poy.err" -error
-command perturb/perturb18.poy -message "'perturb' using 'resample' under default, ERROR expected" -stderr "perturb/stderr/perturb18.poy.err" -error
-command perturb/perturb19.poy -message "'perturb' using 'resample' under default, ERROR expected" -stderr "perturb/stderr/perturb19.poy.err" -error
-command perturb/perturb20.poy -message "default 'perturb' with specified values and multiple 'swap' arguments for fas, ss, aa" -stderr "perturb/stderr/perturb20.poy.err"
-command perturb/perturb21.poy -message "default 'perturb' with specified swap, ratchet and iterations values and multiple 'swap' arguments for fas, ss, and aa" 
-command perturb/perturb22.poy -message "default 'perturb' with specified swap, ratchet, iterations, and transform values and multiple 'swap' arguments for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "perturb/stderr/FILENAME1_FILENAME2_FILENAME3.perturb22.poy.err"
-command perturb/perturb24.poy -message "'perturb' using 'resample' without specifying lident value, ERROR expected" -stderr "perturb/stderr/perturb24.poy.err" -error
-command perturb/perturb26.poy -message "'perturb' using 'resample' with specifying values for fas, aa, ss" -stderr "perturb/stderr/perturb26.poy.err"
-command perturb/perturb27.poy -message "'perturb' using 'resample' with values in reverse order, ERROR expected" -stderr "perturb/stderr/perturb27.poy.err" -error
-command perturb/perturb31.poy -message "simple 'build' and 'perturb' with multiple dynamic homology characters for fas and aa" -stderr "perturb/stderr/perturb31.poy.err"
-command report/report.poy -stdout "./report/stdout/report.out" -message "Build with fas and 30.ss and Report with default setting report.poy" 
-command report/report1.poy -message "Build with fas and 30.ss and Report to a file report1.poy" -stdout "./report/stdout/report1.out"
-command report/report10.poy -message "Build with fas report clades report10.poy" -stdout "./report/stdout/report10.out"
-command report/report12.poy -message "Build 3 trees with fuse .fas and report consensus with integer44 Expect under 50 Error report12.poy" -stderr "./report/stderr/report12.err" -error
-command report/report14.poy -message "Build with fas and 30.ss report with graphconsensus Majority rules 88 report14.poy" -stdout "./report/stdout/report14.out"
-command report/report15.poy -message "Build with fas and 30.ss and report with graphconsensus Majority rules 44 EXPECT under 50 report15.poy" -stderr "./report/stderr/report15.err" -error
-command report/report16.poy -message "Build 3 trees with fas and 30.ss and report with graphconsensus to a ps file report16.poy" -stdout "./report/stdout/report16.out"
-command report/report17.poy -message "Build 3 trees with fas and 30.ss and report with graphsupports for jackknife to screen report17.poy" 
-command report/report18.poy -message "Build 3 with  fas and 30.ss trees and fas report with graphsupports for jackknife ps file report18.poy" -stdout "./report/stdout/report18.out"
-command report/report19.poy -message "Build 3 trees with fas and 30.ss report with graphsupports for bootstrap to screen report19.poy" -stdout "./report/stdout/report19.poy.out"
-command report/report2.poy -message "Build with fas and 30.ss and Report cross_references defaults report2.poy" 
-command report/report20.poy -message "Build 3 trees fas and 30.ss report with graphsupports for bootstrap to ps file report20.poy" -stdout "./report/stdout/report20.out"
-command report/report22.poy -message "Build 3 trees fas and 30.ss report with graphsupports for bremer to ps file report22.poy" 
-command report/report23.poy -message "Build 3 trees fas and 30.ss report graphtrees to screen report23.poy" -stdout "./report/stdout/report23.out"
-command report/report24.poy -message "Build 3 trees fas and 30.ss report terminals report24.poy" -stdout "./report/stdout/report24.out"
-command report/report25.poy -message "Build 3 trees fas and 30.ss report terminals report25.poy" -stdout "./report/stdout/report25.out"
-command report/report26.poy -message "Build 3 trees fas and 30.ss report terminals report26.poy" -stdout "./report/stdout/report26.out"
-command report/report27.poy -message "Build 3 trees fas and 30.ss report terminals report27.poy" -stdout "./report/stdout/report27.out"
-command report/report27.poy -message "Build and report trees: cost  fas and 30.ss report terminals report27.poy" -stdout "./report/stdout/report27.out"
-command report/report29.poy -message "Build  report trees: margin report29.poy" -stdout "./report/stdout/report29.out"
-command report/report3.poy -message "Build with 1.fas and Report cross_references: names report3.poy" -stdout "./report/stdout/report3.out"
-command report/report30.poy -message "Build  report trees: nomargin report30.poy" -stdout "./report/stdout/report30.out"
-command report/report31.poy -message "Build  report trees: collapse report31.poy" -stdout "./report/stdout/report31.out"
-command report/report32.poy -message "Build  report trees: collapse false 32.poy" -stdout "./report/stdout/report32.out"
-command report/report33.poy -message "Build  report implied alignments 33.poy" -stdout "./report/stdout/report33.out"
-command report/report34.poy -message "Build  report implied alignments 34.poy" -stdout "./report/stdout/report34.out"
-command report/report39.poy -message "Build  transform using static_approx, and report as a phatwinclad file 39.poy" -stdout "./report/stdout/report39.out"
-command report/report4.poy -message "Build with fas and 30.ss Report data report4.poy" 
-command report/report40.poy -message "Build  and report diagnosis to screen 40.poy" -stdout "./report/stdout/report40.poy.out"
-command report/report41.poy  -message "Build and report diagnosis to file 41.poy" -stderr "./report/stderr/report41.poy.err"
-command report/report44.poy -message "Build  transform to static characters, and report memory report44.poy" 
-command report/report46.poy  -message "Build  report as a phatwinclad file 46.poy" -stdout "./report/stdout/report46.poy.out"
-command report/report6.poy -message "Build with fas and 30.ss and report with terminals report6.poy" 
-command report/report7.poy -message "Build with fas and 30.ss and report with treestats report7.poy" 
-command report/report8.poy -message "Build with fas and 30.ss and report trees directed to a file report8.poy" -stdout "./report/stdout/report8.out"
-command report/report9.poy -message "Build with fas and 30.ss and report asciitrees default report9.poy" 
-command search/search01.poy -message "'search' under defaults without reading data files; expect error" -error
-command search/search02.poy -message "'search' under defaults" 
-command search/search03.poy -message "'search' max_time:0:0:05" 
-command search/search04.poy -message "'search' with memory:mb:800" 
-command search/search06.poy -message "'search' with 'hits:25'" 
-command search/search07.poy -message "'search' target_cost:4300" 
-command search/search08.poy -message "'search' with max_time:0:0:15, min_time:0:0:5" 
-command search/search09.poy -message "'search' with hits:5, max_time:0:0:25" 
-command search/search10.poy -message "'search' max_time:0:015'" 
-command search_static/search_static01.poy -message "'search' under defaults without reading data files; expect error; static homology characters only" -error
-command search_static/search_static02.poy -message "'search' under defaults; static homology characters only" 
-command search_static/search_static03.poy -message "'search' max_time:0:0:05; static homology characters only" 
-command search_static/search_static04.poy -message "'search' with memory:mb:800; static homology characters only" 
-command search_static/search_static05.poy -message "'search' with min_time:0:0:15 argument; static homology characters only" 
-command search_static/search_static06.poy -message "'search' with 'hits:25; static homology characters only'" 
-command search_static/search_static07.poy -message "'search' target_cost:4300; static homology characters only" 
-command search_static/search_static08.poy -message "'search' with max_time:0:0:15, min_time:0:0:5; static homology characters only"
-command search_static/search_static09.poy -message "'search' with hits:5, max_time:0:0:25; static homology characters only" 
-command search_static/search_static10.poy -message "'search' max_time:0:0:15'; static homology characters only" 
-command select/select01.poy -message "'select' terminals using terminals file with identifiers" -stderr "select/stderr/select01.poy.err" -stdout "select/stdout/select01.poy.out"
-command select/select02.poy -message "'select' terminals using terminals file without identifiers" -stderr "select/stderr/select02.poy.err" -stdout "select/stdout/select02.poy.out"
-command select/select04.poy -message "'select' terminals based terminal names 1" -stderr "select/stderr/select04.poy.err" -stdout "select/stdout/select04.poy.out"
-command select/select05.poy -message "'select' terminals based terminal names 2" -stderr "select/stderr/select05.poy.err" -stdout "select/stdout/select05.poy.out"
-command select/select07.poy -message "'select' under default" -stdout "select/stdout/select07.poy.out"
-command select/select08.poy -message "'select' optimal trees" -stdout "select/stdout/select08.poy.out"
-command select/select09.poy -message "'select' best trees" -stdout "select/stdout/select09.poy.out"
-command select/select10.poy -message "'select' 0 trees = removing trees from memory" -stdout "select/stdout/select10.poy.out"
-command select/select11.poy -message "'select' more best trees than available" -stdout "select/stdout/select11.poy.out"
-command select/select12.poy -message "'select' suboptimal trees" -stdout "select/stdout/select12.poy.out"
-command select/select13.poy -message "'select' decimal number of best trees; ERROR expected" -stderr "select/stderr/select13.poy.err" -error
-command select/select14.poy -message "'select' negative number of best trees; ERROR expected" -stdout "select/stderr/select14.poy.err" -error
-command select/select15.poy -message "'select' unique trees" -stdout "select/stdout/select15.poy.out"
-command set/set01.poy -message "'set' under defaults, just to see if works"
-command set/set02.poy -message "setting 'history', just to see if works"
-command set/set04.poy -message "setting and verifying rooting" -stdout "set/stdout/set04.out"
-command set/set05.poy -message "test 'normal_do'" -diff "set/xml/set05.poy.xml"
-command set/set06.poy -message "test 'exhaustive_do'" -diff "set/xml/set06.poy.xml"
-command set/set07.poy -message "test 'normal_do' and 'exhaustive_do'" -diff "set/xml/set07.poy.xml"
-command set/set08.poy -message "test 'iterative'"
-command swap/swap01.poy -message "'swap' under defaults without build, ERROR expected" -stderr "swap/stderr/swap01.poy.err"  -error
-command swap/swap02.poy -message "'swap' under defaults for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap02.poy.err"
-command swap/swap03.poy -message "'swap' with 'alternate' for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap03.poy.err"
-command swap/swap04.poy -message "'swap' with 'spr' for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap04.poy.err"
-command swap/swap05.poy -message "'swap' with 'tbr' for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap05.poy.err"
-command swap/swap07.poy -message "'swap' default under 'around' trajectory for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap07.poy.err"
-command swap/swap08.poy -message "alternate 'swap' under 'around' trajectory for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap08.poy.err"
-command swap/swap09.poy -message "simulated annealing without specifying values; ERROR expected" -stderr "swap/stderr/swap09.poy.err" -error
-command swap/swap10.poy -message "simulated annealing without specifying values; ERROR expected" -stderr "swap/stderr/swap10.poy.err" -error
-command swap/swap11.poy -message "alternate 'swap' under 'around' trajectory for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap11.poy.err"
-command swap/swap13.poy -message "tree drifting without specifying values, ERROR expected" -stderr "swap/stderr/swap13.poy.err"  -error
-command swap/swap14.poy -message "tree drifting without specifying values, ERROR expected" -stderr "swap/stderr/swap14.poy.err" -error
-command swap/swap15.poy -message "'swap' with 'alternate' and braking edge once for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" 
-command swap/swap16.poy -message "'swap' with 'tbr' and random braking edge for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap16.poy.err"
-command swap/swap17.poy -message "'swap' with 'spr' and length dependent edge braking for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap17.poy.err"
-command swap/swap18.poy -message "'swap' under default constraint for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap18.poy.err"
-command swap/swap21.poy -message "'swap' under under default with specified 'depth' for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap21.poy.err"
-command swap/swap22.poy -message "'swap' using all join positions for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap22.poy.err"
-command swap/swap23.poy -message "sectorial search without specifying value for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap23.poy.err"
-command swap/swap24.poy -message "sectorial search for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap24.poy.err"
-command swap/swap25.poy -message "sectorial search with float value, ERROR expected" -stderr "swap/stderr/swap25.poy.err"  -error
-command swap/swap26.poy -message "sectorial search with float value, ERROR expected" -stderr "swap/stderr/swap26.poy.err" -error
-command swap/swap27.poy -message "'swap' under default 'bfs' for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap27.poy.err"
-command swap/swap28.poy -message "'swap' under 'bfs' with integer value for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap28.poy.err"
-command swap/swap29.poy -message "'swap' under 'bfs' with negative integer value; ERROR expected" -stderr "swap/stderr/swap29.poy.err" -error
-command swap/swap30.poy -message "'swap' under 'bfs' with float value; ERROR expected" -stderr "swap/stderr/swap30.poy.err" -error
-command swap/swap31.poy -message "'swap' with 'alternate' under 'bfs' for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap31.poy.err"
-command swap/swap32.poy -message "'swap' under defaults with timeout"
-command swap/swap33.poy -message "'swap' under defaults with timeout but not specifying seconds, ERROR expected" -stderr "swap/stderr/swap33.poy.err" -error
-command swap/swap34.poy -message "'swap' under defaults with timeout but negative seconds, ERROR expected" -stderr "swap/stderr/swap34.poy.err" -error
-command swap/swap35.poy -message "'swap' and printing intermediate trees"
-command swap/swap36.poy -message "'swap' evaluating suboptimal trees specified by integer for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap36.poy.err"
-command swap/swap37.poy -message "'swap' evaluating suboptimal trees specified by float for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap37.poy.err"
-command swap/swap38.poy -message "'swap' evaluating suboptimal trees specified by negative number, ERROR expected" -stderr "swap/stderr/swap38.poy.err" -error
-command swap/swap39.poy -message "'swap' with  number number of trees to retain" -stderr "swap/stderr/swap39.poy.err"
-command swap/swap40.poy -message "'swap' with  number of trees to retain by float; ERROR expected" -stderr "swap/stderr/swap40.poy.err" -error
-command swap/swap41.poy -message "'swap' with  number of trees to retain by negative integer; ERROR expected" -stderr "swap/stderr/swap41.poy.err" -error
-command swap/swap42.poy -message "'swap' argument combination 1 for FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "swap/stderr/FILENAME1_FILENAME2_FILENAME3.swap42.poy.err"
-command swap/swap43.poy -message "'swap' and outputting visited trees" 
-command transform/transform.poy -message "transform all tcm(4,2) with fasta, ss, and aa files transform.poy" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "./transform/stderr/FILENAME1_FILENAME2_FILENAME3.transform.err" 
-command transform/transform1.poy -message "transform all gap_opening with fasta, ss, and aa files transform1.poy" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "./transform/stderr/FILENAME1_FILENAME2_FILENAME3.transform1.err"
-command transform/transform11.poy -message "transform using static_approx with fasta transform11.poy" -inputfile "fas" -stderr "./transform/stderr/FILENAME1.transform11.err"
-command transform/transform12.poy -message "Transform fas, ss and aa combinations with static_approx:keep (Transform12) FILENAME1" -inputfile "fas" -stderr "./transform/stderr/FILENAME1.transform12.err" -stdout "./transform/stdout/FILENAME1.transform12.out"
-command transform/transform17.poy -message "Transform fas, ss and aa combinations with tcm (Transform17) FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "./transform/stderr/FILENAME1_FILENAME2_FILENAME3.transform17.err"
-command transform/transform19.poy -message "Transform fas, ss and aa combinations with weight integer (Transform19) FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "./transform/stderr/FILENAME1_FILENAME2_FILENAME3.transform19.err"
-command transform/transform21.poy -message "test read and transform weightfactor float with fasta transform21.poy" -inputfile "fas" -stderr "./transform/stderr/FILENAME1.transform21.err"
-command transform/transform23.poy -message "Transform fas, ss and aa combinations with weight float (Transform23) FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "./transform/stderr/FILENAME1_FILENAME2_FILENAME3.transform23.err"
-command transform/transform25.poy -message "Transform fas, ss and aa combinations with weightfactor integer (Transform25) FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "./transform/stderr/FILENAME1_FILENAME2_FILENAME3.transform25.err"
-command transform/transform30.poy -message "Transform custom alphabet to breakinv (Transform30)" -stderr "./transform/stderr/transform30.err"
-command transform/transform31.poy -message "Transform custom alphabet to breakinv, dyamic_pam, locus_breakpoint:50 (Transform31)" -stderr "./transform/stderr/transform31.err"
-command transform/transform32.poy -message "Transform custom alphabet to breakinv, dyamic_pam, approx true (Transform32)" -stderr "./transform/stderr/transform32.err"
-command transform/transform33.poy -message "Transform custom alphabet to breakinv, dyamic_pam, circular true (Transform33)" -stderr "./transform/stderr/transform33.err"
-command transform/transform34.poy -message "Transform custom alphabet to breakinv, dyamic_pam,locus_inversion (Transform34)" -stderr "./transform/stderr/transform34.err"
-command transform/transform35.poy -message "Transform custom alphabet to breakinv, dyamic_pam,locus_indel (Transform35)" -stderr "./transform/stderr/transform35.err"
-command transform/transform36.poy -message "Transform custom alphabet to breakinv, dyamic_pam,median (Transform36)" -stderr "./transform/stderr/transform36.err"
-command transform/transform37.poy -message "Transform custom alphabet to breakinv, dyamic_pam,min_seed_length (Transform37)" -stderr "./transform/stderr/transform37.err"
-command transform/transform38.poy -message "Transform custom alphabet to breakinv, dyamic_pam,min_loci_len (Transform38)" -stderr "./transform/stderr/transform38.err"
-command transform/transform39.poy -message "Transform custom alphabet to breakinv, dyamic_pam, min_rearrangement_len (Transform39)" -stderr "./transform/stderr/transform39.err"
-command transform/transform40.poy -message "Transform custom alphabet to breakinv, dyamic_pam, swap_med  (Transform40)" -stderr "./transform/stderr/transform40.err"
-command transform/transform42.poy -message "Transform with dyamic_pam defaults annotated chromosome data (Transform42) FILENAME1" -inputfile "ann" -stderr "./transform/stderr/FILENAME1.transform42.err"
-command transform/transform43.poy -message "Transform with dyamic_pam locus_breakpoint annotated chromosome data (Transform43) FILENAME1" -inputfile "ann" -stderr "./transform/stderr/FILENAME1.transform43.err"
-command transform/transform44.poy -message "Transform with dyamic_pam med_approx annotated chromosome data (Transform44) FILENAME1" -inputfile "ann" -stderr "./transform/stderr/FILENAME1.transform44.err"
-command transform/transform45.poy -message "Transform with dyamic_pam circular annotated chromosome data (Transform45) FILENAME1" -inputfile "ann" -stderr "./transform/stderr/FILENAME1.transform45.err"
-command transform/transform46.poy -message "Transform with dyamic_pam locus_inversion annotated chromosome data (Transform46) FILENAME1" -inputfile "ann" -stderr "./transform/stderr/FILENAME1.transform46.err"
-command transform/transform47.poy -message "Transform with dyamic_pam locus_indel annotated chromosome data (Transform47) FILENAME1" -inputfile "ann" -stderr "./transform/stderr/FILENAME1.transform47.err"
-command transform/transform48.poy -message "Transform with dyamic_pam median annotated chromosome data (Transform48) FILENAME1" -inputfile "ann" -stderr "./transform/stderr/FILENAME1.transform48.err"
-command transform/transform49.poy -message "Transform with dyamic_pam min_seed_length annotated chromosome data (Transform49) FILENAME1" -inputfile "ann" -stderr "./transform/stderr/FILENAME1.transform49.err"
-command transform/transform50.poy -message "Transform with dyamic_pam locus_breakpoint and locus_inversion annotated chromosome data EXPECT ERROR(Transform50) FILENAME1" -inputfile "ann" -stderr "./transform/stderr/FILENAME1.transform50.err" -error
-command transform/transform51.poy -message "Transform with dyamic_pam min_rearrangement_len annotated chromosome data (Transform51) FILENAME1" -inputfile "ann" -stderr "./transform/stderr/FILENAME1.transform51.err"
-command transform/transform52.poy -message "Transform with dyamic_pam swap_med annotated chromosome data (Transform52) FILENAME1" -inputfile "ann" -stderr "./transform/stderr/FILENAME1.transform52.err"
-command transform/transform54.poy -message "Transform with dyamic_pam default unannotated chromosome data (Transform54) FILENAME1" -inputfile "unann" -stderr "./transform/stderr/FILENAME1.transform54.err"
-command transform/transform55.poy -message "Transform with dyamic_pam locus_breakpoint unannotated chromosome data (Transform55) FILENAME1" -inputfile "unann" -stderr "./transform/stderr/FILENAME1.transform55.err"
-command transform/transform56.poy -message "Transform with dyamic_pam med_approx unannotated chromosome data (Transform56) FILENAME1" -inputfile "unann" -stderr "./transform/stderr/FILENAME1.transform56.err"
-command transform/transform57.poy -message "Transform with dyamic_pam circular unannotated chromosome data (Transform57) FILENAME1" -inputfile "unann" -stderr "./transform/stderr/FILENAME1.transform57.err"
-command transform/transform58.poy -message "Transform with dyamic_pam locus_inversion unannotated chromosome data (Transform58) FILENAME1" -inputfile "unann" -stderr "./transform/stderr/FILENAME1.transform58.err"
-command transform/transform59.poy -message "Transform with dyamic_pam locus_indel unannotated chromosome data (Transform59) FILENAME1" -inputfile "unann" -stderr "./transform/stderr/FILENAME1.transform59.err"
-command transform/transform6.poy -message "Transform fas combinations with all auto_sequence_partition (Transform6) FILENAME1" -inputfile "fas" -stderr "./transform/stderr/FILENAME1.transform6.err"
-command transform/transform6.poy -message "transform with auto_sequence_partition and build with fasta  transform6.poy" -inputfile "fas" -stderr "./transform/stderr/FILENAME1.transform6.err"
-command transform/transform60.poy -message "Transform with dyamic_pam median unannotated chromosome data (Transform60) FILENAME1" -inputfile "unann" -stderr "./transform/stderr/FILENAME1.transform60.err"
-command transform/transform61.poy -message "Transform with dyamic_pam min_seed_length unannotated chromosome data (Transform61) FILENAME1" -inputfile "unann" -stderr "./transform/stderr/FILENAME1.transform61.err"
-command transform/transform62.poy -message "Transform with dyamic_pam min_rearrangement_len unannotated chromosome data (Transform62) FILENAME1" -inputfile "unann" -stderr "./transform/stderr/FILENAME1.transform62.err"
-command transform/transform63.poy -message "Transform with dyamic_pam min_rearrangement_len using float unannotated chromosome data EXPECT ERROR (Transform63) FILENAME1" -inputfile "unann" -stderr "./transform/stderr/FILENAME1.transform63.err" -error
-command transform/transform64.poy -message "Transform with dyamic_pam swap_med unannotated chromosome data (Transform64) FILENAME1" -inputfile "unann" -stderr "./transform/stderr/FILENAME1.transform64.err"
-command transform/transform66.poy -message "Transform with dyamic_pam default genome data (Transform66) FILENAME1" -inputfile "gen" -stderr "./transform/stderr/FILENAME1.transform66.err"
-command transform/transform67.poy -message "Transform with dyamic_pam chrom_hom genome data (Transform67) FILENAME1" -inputfile "gen" -stderr "./transform/stderr/FILENAME1.transform67.err"
-command transform/transform68.poy -message "Transform with dyamic_pam chrom_indel genome data (Transform68) FILENAME1" -inputfile "gen" -stderr "./transform/stderr/FILENAME1.transform68.err"
-command transform/transform69.poy -message "Transform with dyamic_pam chrom_breakpoint genome data (Transform69) FILENAME1" -inputfile "gen" -stderr "./transform/stderr/FILENAME1.transform69.err"
-command transform/transform7.poy -message "Transform fas with fixedstates (Transform7) FILENAME1" -inputfile "fas" -stdout "./transform/stdout/FILENAME1.transform7.stdout" -stderr "./transform/stderr/FILENAME1.transform7.err"
-command transform/transform71.poy -message "Transform seq to chromosome (Transform71)" -inputfile "fas" -stderr "./transform/stderr/FILENAME1.transform71.err"-message "Transform static with tcm:(1,1) Expect Error(Transform_static)" -command ./transform_static/transform_static.poy -stderr "./transform_static/stderr/transform_static.err" -error
-command transform/transform8.poy -message "Transform fas, ss and aa combinations with gap_opening (Transform8) FILENAME1 FILENAME2 FILENAME3" -inputfile "fas" -inputfile "ss" -inputfile "aa" -stderr "./transform/stderr/FILENAME1_FILENAME2_FILENAME3.transform8.err"
-command transform/transform9.poy -message "Transform fas, ss and aa combinations with multi_static_approx (Transform9) FILENAME1" -inputfile "fas" -stderr "./transform/stderr/FILENAME1.transform9.err"
-command transform_static/transform10_static.poy -message "Transform static prealigned Expect Error (Transform10_static)" -stderr "./transform_static/stderr/transform10_static.err" -error
-command transform_static/transform17_static.poy -message "Transform static with all tcm (Transform17_static)" -stderr "./transform_static/stderr/transform17_static.err"
-command transform_static/transform19_static.poy -message "Transform static with all weight integer (Transform19_static)" -stderr "./transform_static/stderr/transform19_static.err"
-command transform_static/transform21_static.poy -message "Transform static with all weightfactor float (Transform21_static)" -stderr "./transform_static/stderr/transform21_static.err"
-command transform_static/transform23_static.poy -message "Transform static with all weight float (Transform23_static)" -stderr "./transform_static/stderr/transform23_static.err"
-command transform_static/transform25_static.poy -message "Transform static with all weightfactor integer (Transform25_static)" -stderr "./transform_static/stderr/transform25_static.err"
-command transform_static/transform7_static.poy -message "Transform static with all fixedstates Expect Error(Transform7_static)" -stdout "./transform_static/stdout/transform7_static.out"
-command transform_static/transform8_static.poy -message "Transform static with all gap_opening Expect Error(Transform8_static)" -stderr "./transform_static/stderr/transform8_static.err"
