1 ###################################################
\r
3 # Makefile for mothur
\r
4 # Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41]
\r
5 # Created: April 16, 2010
\r
7 ###################################################
\r
16 # if you do not want to use the readline library set to no, default yes.
\r
17 # make sure you have the library installed
\r
21 ifeq ($(strip $(USEREADLINE)),yes)
\r
22 CC_OPTIONS += -DUSE_READLINE
\r
31 ifeq ($(strip $(USEMPI)),yes)
\r
33 CC_OPTIONS += -DUSE_MPI
\r
37 # INCLUDE directories for mothur
\r
47 ./sharedutilities.o\
\r
48 ./treegroupscommand.o\
\r
49 ./bootstrapsharedcommand.o\
\r
50 ./matrixoutputcommand.o\
\r
51 ./getoturepcommand.o\
\r
52 ./screenseqscommand.o\
\r
56 ./readdistcommand.o\
\r
62 ./needlemanoverlap.o\
\r
74 ./unifracweightedcommand.o\
\r
77 ./unifracunweightedcommand.o\
\r
78 ./getsabundcommand.o\
\r
79 ./getrabundcommand.o\
\r
82 ./sharedanderbergs.o\
\r
88 ./libshuffcommand.o\
\r
90 ./sharedbraycurtis.o\
\r
91 ./sharedkulczynski.o\
\r
93 ./sharedkulczynskicody.o\
\r
94 ./sharedmorisitahorn.o\
\r
99 ./consensuscommand.o\
\r
100 ./heatmapsimcommand.o\
\r
103 ./filterseqscommand.o\
\r
106 ./sharedjackknife.o\
\r
107 ./sharedmarczewski.o\
\r
110 ./parsimonycommand.o\
\r
112 ./seqsummarycommand.o\
\r
113 ./chimeraccodecommand.o\
\r
114 ./chimerabellerophoncommand.o\
\r
115 ./chimeracheckcommand.o\
\r
116 ./chimeraslayercommand.o\
\r
117 ./chimerapintailcommand.o\
\r
118 ./chimeraseqscommand.o\
\r
119 ./sharedlistvector.o\
\r
122 ./sharedsobscollectsummary.o\
\r
123 ./deconvolutecommand.o\
\r
124 ./listseqscommand.o\
\r
125 ./getseqscommand.o\
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126 ./removeseqscommand.o\
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128 ./binsequencecommand.o\
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129 ./distancecommand.o\
\r
131 ./averagelinkage.o\
\r
136 ./clustercommand.o\
\r
138 ./collectcommand.o\
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139 ./collectsharedcommand.o\
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140 ./commandoptionparser.o\
\r
141 ./completelinkage.o\
\r
149 ./makegroupcommand.o\
\r
150 ./chopseqscommand.o\
\r
151 ./clearcutcommand.o\
\r
152 ./catchallcommand.o\
\r
153 ./splitabundcommand.o\
\r
155 ./clustersplitcommand.o\
\r
156 ./weightedlinkage.o\
\r
163 ./nameassignment.o\
\r
172 ./rarefactcommand.o\
\r
173 ./rarefactsharedcommand.o\
\r
183 ./sharedordervector.o\
\r
184 ./sharedrabundvector.o\
\r
185 ./sharedsabundvector.o\
\r
187 ./sharedsorabund.o\
\r
188 ./sharedsorclass.o\
\r
195 ./summarycommand.o\
\r
196 ./summarysharedcommand.o\
\r
198 ./validcalculator.o\
\r
199 ./validparameter.o\
\r
201 ./readtreecommand.o\
\r
202 ./reversecommand.o\
\r
203 ./trimseqscommand.o\
\r
207 ./mergefilecommand.o\
\r
210 ./preclustercommand.o\
\r
211 ./otuhierarchycommand.o\
\r
213 ./getgroupcommand.o\
\r
214 ./getlabelcommand.o\
\r
215 ./secondarystructurecommand.o\
\r
217 ./parselistscommand.o\
\r
219 ./chimeracheckrdp.o\
\r
220 ./hclustercommand.o\
\r
222 ./getlistcountcommand.o\
\r
225 ./taxonomyequalizer.o\
\r
226 ./phylotypecommand.o\
\r
227 ./classifyseqscommand.o\
\r
228 ./classifyotucommand.o\
\r
229 ./parsesffcommand.o\
\r
232 ./phylodiversity.o\
\r
233 ./phylodiversitycommand.o\
\r
244 ./mgclustercommand.o\
\r
245 ./getsharedotucommand.o\
\r
247 ./chimerarealigner.o\
\r
255 ./setlogfilecommand.o
\r
256 $(CC) $(LNK_OPTIONS) \
\r
257 ./sharedutilities.o\
\r
258 ./treegroupscommand.o\
\r
259 ./bootstrapsharedcommand.o\
\r
260 ./matrixoutputcommand.o\
\r
261 ./getoturepcommand.o\
\r
262 ./screenseqscommand.o\
\r
265 ./readotucommand.o\
\r
266 ./readdistcommand.o\
\r
267 ./commandfactory.o\
\r
272 ./needlemanoverlap.o\
\r
284 ./unifracweightedcommand.o\
\r
287 ./unifracunweightedcommand.o\
\r
288 ./getsabundcommand.o\
\r
289 ./getrabundcommand.o\
\r
292 ./sharedanderbergs.o\
\r
297 ./heatmapcommand.o\
\r
298 ./libshuffcommand.o\
\r
300 ./sharedbraycurtis.o\
\r
301 ./sharedkulczynski.o\
\r
303 ./sharedkulczynskicody.o\
\r
304 ./sharedmorisitahorn.o\
\r
309 ./consensuscommand.o\
\r
310 ./heatmapsimcommand.o\
\r
313 ./filterseqscommand.o\
\r
316 ./sharedjackknife.o\
\r
317 ./sharedmarczewski.o\
\r
320 ./parsimonycommand.o\
\r
322 ./seqsummarycommand.o\
\r
323 ./chimeraccodecommand.o\
\r
324 ./chimerabellerophoncommand.o\
\r
325 ./chimeracheckcommand.o\
\r
326 ./chimeraslayercommand.o\
\r
327 ./chimerapintailcommand.o\
\r
328 ./chimeraseqscommand.o\
\r
329 ./sharedlistvector.o\
\r
332 ./sharedsobscollectsummary.o\
\r
333 ./deconvolutecommand.o\
\r
334 ./listseqscommand.o\
\r
335 ./getseqscommand.o\
\r
336 ./removeseqscommand.o\
\r
338 ./binsequencecommand.o\
\r
339 ./distancecommand.o\
\r
341 ./averagelinkage.o\
\r
346 ./clustercommand.o\
\r
348 ./collectcommand.o\
\r
349 ./collectsharedcommand.o\
\r
350 ./commandoptionparser.o\
\r
351 ./completelinkage.o\
\r
359 ./makegroupcommand.o\
\r
360 ./chopseqscommand.o\
\r
361 ./clearcutcommand.o\
\r
362 ./catchallcommand.o\
\r
363 ./splitabundcommand.o\
\r
365 ./clustersplitcommand.o\
\r
366 ./weightedlinkage.o\
\r
373 ./nameassignment.o\
\r
382 ./rarefactcommand.o\
\r
383 ./rarefactsharedcommand.o\
\r
393 ./sharedordervector.o\
\r
394 ./sharedrabundvector.o\
\r
395 ./sharedsabundvector.o\
\r
397 ./sharedsorabund.o\
\r
398 ./sharedsorclass.o\
\r
405 ./summarycommand.o\
\r
406 ./summarysharedcommand.o\
\r
408 ./validcalculator.o\
\r
409 ./validparameter.o\
\r
411 ./readtreecommand.o\
\r
412 ./reversecommand.o\
\r
413 ./trimseqscommand.o\
\r
417 ./mergefilecommand.o\
\r
420 ./preclustercommand.o\
\r
421 ./otuhierarchycommand.o\
\r
423 ./getgroupcommand.o\
\r
424 ./getlabelcommand.o\
\r
425 ./secondarystructurecommand.o\
\r
427 ./parselistscommand.o\
\r
429 ./chimeracheckrdp.o\
\r
430 ./hclustercommand.o\
\r
432 ./getlistcountcommand.o\
\r
435 ./taxonomyequalizer.o\
\r
436 ./phylotypecommand.o\
\r
437 ./classifyseqscommand.o\
\r
438 ./classifyotucommand.o\
\r
439 ./parsesffcommand.o\
\r
442 ./phylodiversity.o\
\r
443 ./phylodiversitycommand.o\
\r
454 ./mgclustercommand.o\
\r
455 ./getsharedotucommand.o\
\r
457 ./chimerarealigner.o\
\r
465 ./setlogfilecommand.o\
\r
470 ./sharedutilities.o\
\r
471 ./treegroupscommand.o\
\r
472 ./bootstrapsharedcommand.o\
\r
473 ./matrixoutputcommand.o\
\r
474 ./getoturepcommand.o\
\r
475 ./screenseqscommand.o\
\r
478 ./readotucommand.o\
\r
479 ./readdistcommand.o\
\r
480 ./commandfactory.o\
\r
485 ./needlemanoverlap.o\
\r
497 ./unifracweightedcommand.o\
\r
500 ./unifracunweightedcommand.o\
\r
501 ./getsabundcommand.o\
\r
502 ./getrabundcommand.o\
\r
505 ./sharedanderbergs.o\
\r
510 ./heatmapcommand.o\
\r
511 ./libshuffcommand.o\
\r
513 ./sharedbraycurtis.o\
\r
514 ./sharedkulczynski.o\
\r
516 ./sharedkulczynskicody.o\
\r
517 ./sharedmorisitahorn.o\
\r
522 ./consensuscommand.o\
\r
523 ./heatmapsimcommand.o\
\r
526 ./filterseqscommand.o\
\r
529 ./sharedjackknife.o\
\r
530 ./sharedmarczewski.o\
\r
533 ./parsimonycommand.o\
\r
535 ./seqsummarycommand.o\
\r
536 ./chimeraccodecommand.o\
\r
537 ./chimerabellerophoncommand.o\
\r
538 ./chimeracheckcommand.o\
\r
539 ./chimeraslayercommand.o\
\r
540 ./chimerapintailcommand.o\
\r
541 ./chimeraseqscommand.o\
\r
542 ./sharedlistvector.o\
\r
545 ./sharedsobscollectsummary.o\
\r
546 ./deconvolutecommand.o\
\r
547 ./listseqscommand.o\
\r
548 ./getseqscommand.o\
\r
549 ./removeseqscommand.o\
\r
551 ./binsequencecommand.o\
\r
552 ./distancecommand.o\
\r
554 ./averagelinkage.o\
\r
559 ./clustercommand.o\
\r
561 ./collectcommand.o\
\r
562 ./collectsharedcommand.o\
\r
563 ./commandoptionparser.o\
\r
564 ./completelinkage.o\
\r
572 ./makegroupcommand.o\
\r
573 ./chopseqscommand.o\
\r
574 ./clearcutcommand.o\
\r
575 ./catchallcommand.o\
\r
576 ./splitabundcommand.o\
\r
578 ./clustersplitcommand.o\
\r
579 ./weightedlinkage.o\
\r
586 ./nameassignment.o\
\r
595 ./rarefactcommand.o\
\r
596 ./rarefactsharedcommand.o\
\r
606 ./sharedordervector.o\
\r
607 ./sharedrabundvector.o\
\r
608 ./sharedsabundvector.o\
\r
610 ./sharedsorabund.o\
\r
611 ./sharedsorclass.o\
\r
618 ./summarycommand.o\
\r
619 ./summarysharedcommand.o\
\r
621 ./validcalculator.o\
\r
622 ./validparameter.o\
\r
624 ./readtreecommand.o\
\r
625 ./reversecommand.o\
\r
626 ./trimseqscommand.o\
\r
630 ./mergefilecommand.o\
\r
633 ./preclustercommand.o\
\r
634 ./otuhierarchycommand.o\
\r
636 ./getgroupcommand.o\
\r
637 ./getlabelcommand.o\
\r
638 ./secondarystructurecommand.o\
\r
640 ./parselistscommand.o\
\r
642 ./chimeracheckrdp.o\
\r
643 ./hclustercommand.o\
\r
645 ./getlistcountcommand.o\
\r
648 ./taxonomyequalizer.o\
\r
649 ./phylotypecommand.o\
\r
650 ./classifyseqscommand.o\
\r
651 ./classifyotucommand.o\
\r
652 ./parsesffcommand.o\
\r
655 ./phylodiversity.o\
\r
656 ./phylodiversitycommand.o\
\r
667 ./mgclustercommand.o\
\r
668 ./getsharedotucommand.o\
\r
670 ./chimerarealigner.o\
\r
678 ./setlogfilecommand.o\
\r
682 #cp mothur ../Release/mothur
\r
685 # Build the parts of mothur
\r
689 # Item # 1 -- sharedutilities --
\r
690 ./sharedutilities.o : sharedutilities.cpp
\r
691 $(CC) $(CC_OPTIONS) sharedutilities.cpp -c $(INCLUDE) -o ./sharedutilities.o
\r
694 # Item # 2 -- treegroupscommand --
\r
695 ./treegroupscommand.o : treegroupscommand.cpp
\r
696 $(CC) $(CC_OPTIONS) treegroupscommand.cpp -c $(INCLUDE) -o ./treegroupscommand.o
\r
699 # Item # 3 -- bootstrapsharedcommand --
\r
700 ./bootstrapsharedcommand.o : bootstrapsharedcommand.cpp
\r
701 $(CC) $(CC_OPTIONS) bootstrapsharedcommand.cpp -c $(INCLUDE) -o ./bootstrapsharedcommand.o
\r
704 # Item # 4 -- matrixoutputcommand --
\r
705 ./matrixoutputcommand.o : matrixoutputcommand.cpp
\r
706 $(CC) $(CC_OPTIONS) matrixoutputcommand.cpp -c $(INCLUDE) -o ./matrixoutputcommand.o
\r
709 # Item # 5 -- getoturepcommand --
\r
710 ./getoturepcommand.o : getoturepcommand.cpp
\r
711 $(CC) $(CC_OPTIONS) getoturepcommand.cpp -c $(INCLUDE) -o ./getoturepcommand.o
\r
714 # Item # 6 -- screenseqscommand --
\r
715 ./screenseqscommand.o : screenseqscommand.cpp
\r
716 $(CC) $(CC_OPTIONS) screenseqscommand.cpp -c $(INCLUDE) -o ./screenseqscommand.o
\r
719 # Item # 7 -- chimera --
\r
720 ./chimera.o : chimera.cpp
\r
721 $(CC) $(CC_OPTIONS) chimera.cpp -c $(INCLUDE) -o ./chimera.o
\r
724 # Item # 8 -- decalc --
\r
725 ./decalc.o : decalc.cpp
\r
726 $(CC) $(CC_OPTIONS) decalc.cpp -c $(INCLUDE) -o ./decalc.o
\r
729 # Item # 9 -- readotucommand --
\r
730 ./readotucommand.o : readotucommand.cpp
\r
731 $(CC) $(CC_OPTIONS) readotucommand.cpp -c $(INCLUDE) -o ./readotucommand.o
\r
734 # Item # 10 -- readdistcommand --
\r
735 ./readdistcommand.o : readdistcommand.cpp
\r
736 $(CC) $(CC_OPTIONS) readdistcommand.cpp -c $(INCLUDE) -o ./readdistcommand.o
\r
739 # Item # 11 -- commandfactory --
\r
740 ./commandfactory.o : commandfactory.cpp
\r
741 $(CC) $(CC_OPTIONS) commandfactory.cpp -c $(INCLUDE) -o ./commandfactory.o
\r
744 # Item # 12 -- alignment --
\r
745 ./alignment.o : alignment.cpp
\r
746 $(CC) $(CC_OPTIONS) alignment.cpp -c $(INCLUDE) -o ./alignment.o
\r
749 # Item # 13 -- alignmentcell --
\r
750 ./alignmentcell.o : alignmentcell.cpp
\r
751 $(CC) $(CC_OPTIONS) alignmentcell.cpp -c $(INCLUDE) -o ./alignmentcell.o
\r
754 # Item # 14 -- gotohoverlap --
\r
755 ./gotohoverlap.o : gotohoverlap.cpp
\r
756 $(CC) $(CC_OPTIONS) gotohoverlap.cpp -c $(INCLUDE) -o ./gotohoverlap.o
\r
759 # Item # 15 -- overlap --
\r
760 ./overlap.o : overlap.cpp
\r
761 $(CC) $(CC_OPTIONS) overlap.cpp -c $(INCLUDE) -o ./overlap.o
\r
764 # Item # 16 -- needlemanoverlap --
\r
765 ./needlemanoverlap.o : needlemanoverlap.cpp
\r
766 $(CC) $(CC_OPTIONS) needlemanoverlap.cpp -c $(INCLUDE) -o ./needlemanoverlap.o
\r
769 # Item # 17 -- blastalign --
\r
770 ./blastalign.o : blastalign.cpp
\r
771 $(CC) $(CC_OPTIONS) blastalign.cpp -c $(INCLUDE) -o ./blastalign.o
\r
774 # Item # 18 -- noalign --
\r
775 ./noalign.o : noalign.cpp
\r
776 $(CC) $(CC_OPTIONS) noalign.cpp -c $(INCLUDE) -o ./noalign.o
\r
779 # Item # 19 -- suffixdb --
\r
780 ./suffixdb.o : suffixdb.cpp
\r
781 $(CC) $(CC_OPTIONS) suffixdb.cpp -c $(INCLUDE) -o ./suffixdb.o
\r
784 # Item # 20 -- suffixnodes --
\r
785 ./suffixnodes.o : suffixnodes.cpp
\r
786 $(CC) $(CC_OPTIONS) suffixnodes.cpp -c $(INCLUDE) -o ./suffixnodes.o
\r
789 # Item # 21 -- suffixtree --
\r
790 ./suffixtree.o : suffixtree.cpp
\r
791 $(CC) $(CC_OPTIONS) suffixtree.cpp -c $(INCLUDE) -o ./suffixtree.o
\r
794 # Item # 22 -- blastdb --
\r
795 ./blastdb.o : blastdb.cpp
\r
796 $(CC) $(CC_OPTIONS) blastdb.cpp -c $(INCLUDE) -o ./blastdb.o
\r
799 # Item # 23 -- nast --
\r
800 ./nast.o : nast.cpp
\r
801 $(CC) $(CC_OPTIONS) nast.cpp -c $(INCLUDE) -o ./nast.o
\r
804 # Item # 24 -- nastreport --
\r
805 ./nastreport.o : nastreport.cpp
\r
806 $(CC) $(CC_OPTIONS) nastreport.cpp -c $(INCLUDE) -o ./nastreport.o
\r
809 # Item # 25 -- boneh --
\r
810 ./boneh.o : boneh.cpp
\r
811 $(CC) $(CC_OPTIONS) boneh.cpp -c $(INCLUDE) -o ./boneh.o
\r
814 # Item # 26 -- efron --
\r
815 ./efron.o : efron.cpp
\r
816 $(CC) $(CC_OPTIONS) efron.cpp -c $(INCLUDE) -o ./efron.o
\r
819 # Item # 27 -- solow --
\r
820 ./solow.o : solow.cpp
\r
821 $(CC) $(CC_OPTIONS) solow.cpp -c $(INCLUDE) -o ./solow.o
\r
824 # Item # 28 -- unifracweightedcommand --
\r
825 ./unifracweightedcommand.o : unifracweightedcommand.cpp
\r
826 $(CC) $(CC_OPTIONS) unifracweightedcommand.cpp -c $(INCLUDE) -o ./unifracweightedcommand.o
\r
829 # Item # 29 -- weighted --
\r
830 ./weighted.o : weighted.cpp
\r
831 $(CC) $(CC_OPTIONS) weighted.cpp -c $(INCLUDE) -o ./weighted.o
\r
834 # Item # 30 -- unweighted --
\r
835 ./unweighted.o : unweighted.cpp
\r
836 $(CC) $(CC_OPTIONS) unweighted.cpp -c $(INCLUDE) -o ./unweighted.o
\r
839 # Item # 31 -- unifracunweightedcommand --
\r
840 ./unifracunweightedcommand.o : unifracunweightedcommand.cpp
\r
841 $(CC) $(CC_OPTIONS) unifracunweightedcommand.cpp -c $(INCLUDE) -o ./unifracunweightedcommand.o
\r
844 # Item # 32 -- getsabundcommand --
\r
845 ./getsabundcommand.o : getsabundcommand.cpp
\r
846 $(CC) $(CC_OPTIONS) getsabundcommand.cpp -c $(INCLUDE) -o ./getsabundcommand.o
\r
849 # Item # 33 -- getrabundcommand --
\r
850 ./getrabundcommand.o : getrabundcommand.cpp
\r
851 $(CC) $(CC_OPTIONS) getrabundcommand.cpp -c $(INCLUDE) -o ./getrabundcommand.o
\r
854 # Item # 34 -- bellerophon --
\r
855 ./bellerophon.o : bellerophon.cpp
\r
856 $(CC) $(CC_OPTIONS) bellerophon.cpp -c $(INCLUDE) -o ./bellerophon.o
\r
859 # Item # 35 -- pintail --
\r
860 ./pintail.o : pintail.cpp
\r
861 $(CC) $(CC_OPTIONS) pintail.cpp -c $(INCLUDE) -o ./pintail.o
\r
864 # Item # 36 -- sharedanderbergs --
\r
865 ./sharedanderbergs.o : sharedanderbergs.cpp
\r
866 $(CC) $(CC_OPTIONS) sharedanderbergs.cpp -c $(INCLUDE) -o ./sharedanderbergs.o
\r
869 # Item # 37 -- venncommand --
\r
870 ./venncommand.o : venncommand.cpp
\r
871 $(CC) $(CC_OPTIONS) venncommand.cpp -c $(INCLUDE) -o ./venncommand.o
\r
874 # Item # 38 -- venn --
\r
875 ./venn.o : venn.cpp
\r
876 $(CC) $(CC_OPTIONS) venn.cpp -c $(INCLUDE) -o ./venn.o
\r
879 # Item # 39 -- fullmatrix --
\r
880 ./fullmatrix.o : fullmatrix.cpp
\r
881 $(CC) $(CC_OPTIONS) fullmatrix.cpp -c $(INCLUDE) -o ./fullmatrix.o
\r
884 # Item # 40 -- heatmap --
\r
885 ./heatmap.o : heatmap.cpp
\r
886 $(CC) $(CC_OPTIONS) heatmap.cpp -c $(INCLUDE) -o ./heatmap.o
\r
889 # Item # 41 -- heatmapcommand --
\r
890 ./heatmapcommand.o : heatmapcommand.cpp
\r
891 $(CC) $(CC_OPTIONS) heatmapcommand.cpp -c $(INCLUDE) -o ./heatmapcommand.o
\r
894 # Item # 42 -- libshuffcommand --
\r
895 ./libshuffcommand.o : libshuffcommand.cpp
\r
896 $(CC) $(CC_OPTIONS) libshuffcommand.cpp -c $(INCLUDE) -o ./libshuffcommand.o
\r
899 # Item # 43 -- nocommands --
\r
900 ./nocommands.o : nocommands.cpp
\r
901 $(CC) $(CC_OPTIONS) nocommands.cpp -c $(INCLUDE) -o ./nocommands.o
\r
904 # Item # 44 -- sharedbraycurtis --
\r
905 ./sharedbraycurtis.o : sharedbraycurtis.cpp
\r
906 $(CC) $(CC_OPTIONS) sharedbraycurtis.cpp -c $(INCLUDE) -o ./sharedbraycurtis.o
\r
909 # Item # 45 -- sharedkulczynski --
\r
910 ./sharedkulczynski.o : sharedkulczynski.cpp
\r
911 $(CC) $(CC_OPTIONS) sharedkulczynski.cpp -c $(INCLUDE) -o ./sharedkulczynski.o
\r
914 # Item # 46 -- sharedlennon --
\r
915 ./sharedlennon.o : sharedlennon.cpp
\r
916 $(CC) $(CC_OPTIONS) sharedlennon.cpp -c $(INCLUDE) -o ./sharedlennon.o
\r
919 # Item # 47 -- sharedkulczynskicody --
\r
920 ./sharedkulczynskicody.o : sharedkulczynskicody.cpp
\r
921 $(CC) $(CC_OPTIONS) sharedkulczynskicody.cpp -c $(INCLUDE) -o ./sharedkulczynskicody.o
\r
924 # Item # 48 -- sharedmorisitahorn --
\r
925 ./sharedmorisitahorn.o : sharedmorisitahorn.cpp
\r
926 $(CC) $(CC_OPTIONS) sharedmorisitahorn.cpp -c $(INCLUDE) -o ./sharedmorisitahorn.o
\r
929 # Item # 49 -- sharedochiai --
\r
930 ./sharedochiai.o : sharedochiai.cpp
\r
931 $(CC) $(CC_OPTIONS) sharedochiai.cpp -c $(INCLUDE) -o ./sharedochiai.o
\r
934 # Item # 50 -- readcolumn --
\r
935 ./readcolumn.o : readcolumn.cpp
\r
936 $(CC) $(CC_OPTIONS) readcolumn.cpp -c $(INCLUDE) -o ./readcolumn.o
\r
939 # Item # 51 -- readotu --
\r
940 ./readotu.o : readotu.cpp
\r
941 $(CC) $(CC_OPTIONS) readotu.cpp -c $(INCLUDE) -o ./readotu.o
\r
944 # Item # 52 -- readphylip --
\r
945 ./readphylip.o : readphylip.cpp
\r
946 $(CC) $(CC_OPTIONS) readphylip.cpp -c $(INCLUDE) -o ./readphylip.o
\r
949 # Item # 53 -- consensuscommand --
\r
950 ./consensuscommand.o : consensuscommand.cpp
\r
951 $(CC) $(CC_OPTIONS) consensuscommand.cpp -c $(INCLUDE) -o ./consensuscommand.o
\r
954 # Item # 54 -- heatmapsimcommand --
\r
955 ./heatmapsimcommand.o : heatmapsimcommand.cpp
\r
956 $(CC) $(CC_OPTIONS) heatmapsimcommand.cpp -c $(INCLUDE) -o ./heatmapsimcommand.o
\r
959 # Item # 55 -- heatmapsim --
\r
960 ./heatmapsim.o : heatmapsim.cpp
\r
961 $(CC) $(CC_OPTIONS) heatmapsim.cpp -c $(INCLUDE) -o ./heatmapsim.o
\r
964 # Item # 56 -- optionparser --
\r
965 ./optionparser.o : optionparser.cpp
\r
966 $(CC) $(CC_OPTIONS) optionparser.cpp -c $(INCLUDE) -o ./optionparser.o
\r
969 # Item # 57 -- filterseqscommand --
\r
970 ./filterseqscommand.o : filterseqscommand.cpp
\r
971 $(CC) $(CC_OPTIONS) filterseqscommand.cpp -c $(INCLUDE) -o ./filterseqscommand.o
\r
974 # Item # 58 -- goodscoverage --
\r
975 ./goodscoverage.o : goodscoverage.cpp
\r
976 $(CC) $(CC_OPTIONS) goodscoverage.cpp -c $(INCLUDE) -o ./goodscoverage.o
\r
979 # Item # 59 -- sequencedb --
\r
980 ./sequencedb.o : sequencedb.cpp
\r
981 $(CC) $(CC_OPTIONS) sequencedb.cpp -c $(INCLUDE) -o ./sequencedb.o
\r
984 # Item # 60 -- sharedjackknife --
\r
985 ./sharedjackknife.o : sharedjackknife.cpp
\r
986 $(CC) $(CC_OPTIONS) sharedjackknife.cpp -c $(INCLUDE) -o ./sharedjackknife.o
\r
989 # Item # 61 -- sharedmarczewski --
\r
990 ./sharedmarczewski.o : sharedmarczewski.cpp
\r
991 $(CC) $(CC_OPTIONS) sharedmarczewski.cpp -c $(INCLUDE) -o ./sharedmarczewski.o
\r
994 # Item # 62 -- aligncommand --
\r
995 ./aligncommand.o : aligncommand.cpp
\r
996 $(CC) $(CC_OPTIONS) aligncommand.cpp -c $(INCLUDE) -o ./aligncommand.o
\r
999 # Item # 63 -- treemap --
\r
1000 ./treemap.o : treemap.cpp
\r
1001 $(CC) $(CC_OPTIONS) treemap.cpp -c $(INCLUDE) -o ./treemap.o
\r
1004 # Item # 64 -- parsimonycommand --
\r
1005 ./parsimonycommand.o : parsimonycommand.cpp
\r
1006 $(CC) $(CC_OPTIONS) parsimonycommand.cpp -c $(INCLUDE) -o ./parsimonycommand.o
\r
1009 # Item # 65 -- parsimony --
\r
1010 ./parsimony.o : parsimony.cpp
\r
1011 $(CC) $(CC_OPTIONS) parsimony.cpp -c $(INCLUDE) -o ./parsimony.o
\r
1014 # Item # 66 -- seqsummarycommand --
\r
1015 ./seqsummarycommand.o : seqsummarycommand.cpp
\r
1016 $(CC) $(CC_OPTIONS) seqsummarycommand.cpp -c $(INCLUDE) -o ./seqsummarycommand.o
\r
1019 # Item # 67 -- chimeraseqscommand --
\r
1020 ./chimeraseqscommand.o : chimeraseqscommand.cpp
\r
1021 $(CC) $(CC_OPTIONS) chimeraseqscommand.cpp -c $(INCLUDE) -o ./chimeraseqscommand.o
\r
1024 # Item # 68 -- sharedlistvector --
\r
1025 ./sharedlistvector.o : sharedlistvector.cpp
\r
1026 $(CC) $(CC_OPTIONS) sharedlistvector.cpp -c $(INCLUDE) -o ./sharedlistvector.o
\r
1029 # Item # 69 -- tree --
\r
1030 ./tree.o : tree.cpp
\r
1031 $(CC) $(CC_OPTIONS) tree.cpp -c $(INCLUDE) -o ./tree.o
\r
1034 # Item # 70 -- readtree --
\r
1035 ./readtree.o : readtree.cpp
\r
1036 $(CC) $(CC_OPTIONS) readtree.cpp -c $(INCLUDE) -o ./readtree.o
\r
1039 # Item # 71 -- sharedsobscollectsummary --
\r
1040 ./sharedsobscollectsummary.o : sharedsobscollectsummary.cpp
\r
1041 $(CC) $(CC_OPTIONS) sharedsobscollectsummary.cpp -c $(INCLUDE) -o ./sharedsobscollectsummary.o
\r
1044 # Item # 72 -- deconvolutecommand --
\r
1045 ./deconvolutecommand.o : deconvolutecommand.cpp
\r
1046 $(CC) $(CC_OPTIONS) deconvolutecommand.cpp -c $(INCLUDE) -o ./deconvolutecommand.o
\r
1049 # Item # 73 -- listseqscommand --
\r
1050 ./listseqscommand.o : listseqscommand.cpp
\r
1051 $(CC) $(CC_OPTIONS) listseqscommand.cpp -c $(INCLUDE) -o ./listseqscommand.o
\r
1054 # Item # 74 -- getseqscommand --
\r
1055 ./getseqscommand.o : getseqscommand.cpp
\r
1056 $(CC) $(CC_OPTIONS) getseqscommand.cpp -c $(INCLUDE) -o ./getseqscommand.o
\r
1059 # Item # 75 -- removeseqscommand --
\r
1060 ./removeseqscommand.o : removeseqscommand.cpp
\r
1061 $(CC) $(CC_OPTIONS) removeseqscommand.cpp -c $(INCLUDE) -o ./removeseqscommand.o
\r
1064 # Item # 76 -- systemcommand --
\r
1065 ./systemcommand.o : systemcommand.cpp
\r
1066 $(CC) $(CC_OPTIONS) systemcommand.cpp -c $(INCLUDE) -o ./systemcommand.o
\r
1069 # Item # 77 -- binsequencecommand --
\r
1070 ./binsequencecommand.o : binsequencecommand.cpp
\r
1071 $(CC) $(CC_OPTIONS) binsequencecommand.cpp -c $(INCLUDE) -o ./binsequencecommand.o
\r
1074 # Item # 78 -- distancecommand --
\r
1075 ./distancecommand.o : distancecommand.cpp
\r
1076 $(CC) $(CC_OPTIONS) distancecommand.cpp -c $(INCLUDE) -o ./distancecommand.o
\r
1079 # Item # 79 -- ace --
\r
1081 $(CC) $(CC_OPTIONS) ace.cpp -c $(INCLUDE) -o ./ace.o
\r
1084 # Item # 80 -- averagelinkage --
\r
1085 ./averagelinkage.o : averagelinkage.cpp
\r
1086 $(CC) $(CC_OPTIONS) averagelinkage.cpp -c $(INCLUDE) -o ./averagelinkage.o
\r
1089 # Item # 81 -- bootstrap --
\r
1090 ./bootstrap.o : bootstrap.cpp
\r
1091 $(CC) $(CC_OPTIONS) bootstrap.cpp -c $(INCLUDE) -o ./bootstrap.o
\r
1094 # Item # 82 -- calculator --
\r
1095 ./calculator.o : calculator.cpp
\r
1096 $(CC) $(CC_OPTIONS) calculator.cpp -c $(INCLUDE) -o ./calculator.o
\r
1099 # Item # 83 -- chao1 --
\r
1100 ./chao1.o : chao1.cpp
\r
1101 $(CC) $(CC_OPTIONS) chao1.cpp -c $(INCLUDE) -o ./chao1.o
\r
1104 # Item # 84 -- cluster --
\r
1105 ./cluster.o : cluster.cpp
\r
1106 $(CC) $(CC_OPTIONS) cluster.cpp -c $(INCLUDE) -o ./cluster.o
\r
1109 # Item # 85 -- clustercommand --
\r
1110 ./clustercommand.o : clustercommand.cpp
\r
1111 $(CC) $(CC_OPTIONS) clustercommand.cpp -c $(INCLUDE) -o ./clustercommand.o
\r
1114 # Item # 86 -- collect --
\r
1115 ./collect.o : collect.cpp
\r
1116 $(CC) $(CC_OPTIONS) collect.cpp -c $(INCLUDE) -o ./collect.o
\r
1119 # Item # 87 -- collectcommand --
\r
1120 ./collectcommand.o : collectcommand.cpp
\r
1121 $(CC) $(CC_OPTIONS) collectcommand.cpp -c $(INCLUDE) -o ./collectcommand.o
\r
1124 # Item # 88 -- collectsharedcommand --
\r
1125 ./collectsharedcommand.o : collectsharedcommand.cpp
\r
1126 $(CC) $(CC_OPTIONS) collectsharedcommand.cpp -c $(INCLUDE) -o ./collectsharedcommand.o
\r
1129 # Item # 89 -- commandoptionparser --
\r
1130 ./commandoptionparser.o : commandoptionparser.cpp
\r
1131 $(CC) $(CC_OPTIONS) commandoptionparser.cpp -c $(INCLUDE) -o ./commandoptionparser.o
\r
1134 # Item # 90 -- completelinkage --
\r
1135 ./completelinkage.o : completelinkage.cpp
\r
1136 $(CC) $(CC_OPTIONS) completelinkage.cpp -c $(INCLUDE) -o ./completelinkage.o
\r
1139 # Item # 91 -- database --
\r
1140 ./database.o : database.cpp
\r
1141 $(CC) $(CC_OPTIONS) database.cpp -c $(INCLUDE) -o ./database.o
\r
1144 # Item # 92 -- engine --
\r
1145 ./engine.o : engine.cpp
\r
1146 $(CC) $(CC_OPTIONS) engine.cpp -c $(INCLUDE) -o ./engine.o
\r
1149 # Item # 93 -- fastamap --
\r
1150 ./fastamap.o : fastamap.cpp
\r
1151 $(CC) $(CC_OPTIONS) fastamap.cpp -c $(INCLUDE) -o ./fastamap.o
\r
1154 # Item # 94 -- fileoutput --
\r
1155 ./fileoutput.o : fileoutput.cpp
\r
1156 $(CC) $(CC_OPTIONS) fileoutput.cpp -c $(INCLUDE) -o ./fileoutput.o
\r
1159 # Item # 95 -- globaldata --
\r
1160 ./globaldata.o : globaldata.cpp
\r
1161 $(CC) $(CC_OPTIONS) globaldata.cpp -c $(INCLUDE) -o ./globaldata.o
\r
1164 # Item # 96 -- groupmap --
\r
1165 ./groupmap.o : groupmap.cpp
\r
1166 $(CC) $(CC_OPTIONS) groupmap.cpp -c $(INCLUDE) -o ./groupmap.o
\r
1169 # Item # 97 -- helpcommand --
\r
1170 ./helpcommand.o : helpcommand.cpp
\r
1171 $(CC) $(CC_OPTIONS) helpcommand.cpp -c $(INCLUDE) -o ./helpcommand.o
\r
1174 # Item # 98 -- inputdata --
\r
1175 ./inputdata.o : inputdata.cpp
\r
1176 $(CC) $(CC_OPTIONS) inputdata.cpp -c $(INCLUDE) -o ./inputdata.o
\r
1179 # Item # 99 -- jackknife --
\r
1180 ./jackknife.o : jackknife.cpp
\r
1181 $(CC) $(CC_OPTIONS) jackknife.cpp -c $(INCLUDE) -o ./jackknife.o
\r
1184 # Item # 100 -- kmer --
\r
1185 ./kmer.o : kmer.cpp
\r
1186 $(CC) $(CC_OPTIONS) kmer.cpp -c $(INCLUDE) -o ./kmer.o
\r
1189 # Item # 101 -- kmerdb --
\r
1190 ./kmerdb.o : kmerdb.cpp
\r
1191 $(CC) $(CC_OPTIONS) kmerdb.cpp -c $(INCLUDE) -o ./kmerdb.o
\r
1194 # Item # 102 -- listvector --
\r
1195 ./listvector.o : listvector.cpp
\r
1196 $(CC) $(CC_OPTIONS) listvector.cpp -c $(INCLUDE) -o ./listvector.o
\r
1199 # Item # 103 -- mothur --
\r
1200 ./mothur.o : mothur.cpp
\r
1201 $(CC) $(CC_OPTIONS) mothur.cpp -c $(INCLUDE) -o ./mothur.o
\r
1204 # Item # 104 -- nameassignment --
\r
1205 ./nameassignment.o : nameassignment.cpp
\r
1206 $(CC) $(CC_OPTIONS) nameassignment.cpp -c $(INCLUDE) -o ./nameassignment.o
\r
1209 # Item # 105 -- npshannon --
\r
1210 ./npshannon.o : npshannon.cpp
\r
1211 $(CC) $(CC_OPTIONS) npshannon.cpp -c $(INCLUDE) -o ./npshannon.o
\r
1214 # Item # 106 -- ordervector --
\r
1215 ./ordervector.o : ordervector.cpp
\r
1216 $(CC) $(CC_OPTIONS) ordervector.cpp -c $(INCLUDE) -o ./ordervector.o
\r
1219 # Item # 107 -- progress --
\r
1220 ./progress.o : progress.cpp
\r
1221 $(CC) $(CC_OPTIONS) progress.cpp -c $(INCLUDE) -o ./progress.o
\r
1224 # Item # 108 -- quitcommand --
\r
1225 ./quitcommand.o : quitcommand.cpp
\r
1226 $(CC) $(CC_OPTIONS) quitcommand.cpp -c $(INCLUDE) -o ./quitcommand.o
\r
1229 # Item # 109 -- rabundvector --
\r
1230 ./rabundvector.o : rabundvector.cpp
\r
1231 $(CC) $(CC_OPTIONS) rabundvector.cpp -c $(INCLUDE) -o ./rabundvector.o
\r
1234 # Item # 110 -- rarecalc --
\r
1235 ./rarecalc.o : rarecalc.cpp
\r
1236 $(CC) $(CC_OPTIONS) rarecalc.cpp -c $(INCLUDE) -o ./rarecalc.o
\r
1239 # Item # 111 -- raredisplay --
\r
1240 ./raredisplay.o : raredisplay.cpp
\r
1241 $(CC) $(CC_OPTIONS) raredisplay.cpp -c $(INCLUDE) -o ./raredisplay.o
\r
1244 # Item # 112 -- rarefact --
\r
1245 ./rarefact.o : rarefact.cpp
\r
1246 $(CC) $(CC_OPTIONS) rarefact.cpp -c $(INCLUDE) -o ./rarefact.o
\r
1249 # Item # 113 -- rarefactcommand --
\r
1250 ./rarefactcommand.o : rarefactcommand.cpp
\r
1251 $(CC) $(CC_OPTIONS) rarefactcommand.cpp -c $(INCLUDE) -o ./rarefactcommand.o
\r
1254 # Item # 114 -- rarefactsharedcommand --
\r
1255 ./rarefactsharedcommand.o : rarefactsharedcommand.cpp
\r
1256 $(CC) $(CC_OPTIONS) rarefactsharedcommand.cpp -c $(INCLUDE) -o ./rarefactsharedcommand.o
\r
1259 # Item # 115 -- sabundvector --
\r
1260 ./sabundvector.o : sabundvector.cpp
\r
1261 $(CC) $(CC_OPTIONS) sabundvector.cpp -c $(INCLUDE) -o ./sabundvector.o
\r
1264 # Item # 116 -- sequence --
\r
1265 ./sequence.o : sequence.cpp
\r
1266 $(CC) $(CC_OPTIONS) sequence.cpp -c $(INCLUDE) -o ./sequence.o
\r
1269 # Item # 117 -- shannon --
\r
1270 ./shannon.o : shannon.cpp
\r
1271 $(CC) $(CC_OPTIONS) shannon.cpp -c $(INCLUDE) -o ./shannon.o
\r
1274 # Item # 118 -- sharedace --
\r
1275 ./sharedace.o : sharedace.cpp
\r
1276 $(CC) $(CC_OPTIONS) sharedace.cpp -c $(INCLUDE) -o ./sharedace.o
\r
1279 # Item # 119 -- sharedchao1 --
\r
1280 ./sharedchao1.o : sharedchao1.cpp
\r
1281 $(CC) $(CC_OPTIONS) sharedchao1.cpp -c $(INCLUDE) -o ./sharedchao1.o
\r
1284 # Item # 120 -- sharedcommand --
\r
1285 ./sharedcommand.o : sharedcommand.cpp
\r
1286 $(CC) $(CC_OPTIONS) sharedcommand.cpp -c $(INCLUDE) -o ./sharedcommand.o
\r
1289 # Item # 121 -- sharedjabund --
\r
1290 ./sharedjabund.o : sharedjabund.cpp
\r
1291 $(CC) $(CC_OPTIONS) sharedjabund.cpp -c $(INCLUDE) -o ./sharedjabund.o
\r
1294 # Item # 122 -- sharedjclass --
\r
1295 ./sharedjclass.o : sharedjclass.cpp
\r
1296 $(CC) $(CC_OPTIONS) sharedjclass.cpp -c $(INCLUDE) -o ./sharedjclass.o
\r
1299 # Item # 123 -- sharedjest --
\r
1300 ./sharedjest.o : sharedjest.cpp
\r
1301 $(CC) $(CC_OPTIONS) sharedjest.cpp -c $(INCLUDE) -o ./sharedjest.o
\r
1304 # Item # 124 -- sharedordervector --
\r
1305 ./sharedordervector.o : sharedordervector.cpp
\r
1306 $(CC) $(CC_OPTIONS) sharedordervector.cpp -c $(INCLUDE) -o ./sharedordervector.o
\r
1309 # Item # 125 -- sharedrabundvector --
\r
1310 ./sharedrabundvector.o : sharedrabundvector.cpp
\r
1311 $(CC) $(CC_OPTIONS) sharedrabundvector.cpp -c $(INCLUDE) -o ./sharedrabundvector.o
\r
1314 # Item # 126 -- sharedsabundvector --
\r
1315 ./sharedsabundvector.o : sharedsabundvector.cpp
\r
1316 $(CC) $(CC_OPTIONS) sharedsabundvector.cpp -c $(INCLUDE) -o ./sharedsabundvector.o
\r
1319 # Item # 127 -- sharedsobs --
\r
1320 ./sharedsobs.o : sharedsobs.cpp
\r
1321 $(CC) $(CC_OPTIONS) sharedsobs.cpp -c $(INCLUDE) -o ./sharedsobs.o
\r
1324 # Item # 128 -- sharedsorabund --
\r
1325 ./sharedsorabund.o : sharedsorabund.cpp
\r
1326 $(CC) $(CC_OPTIONS) sharedsorabund.cpp -c $(INCLUDE) -o ./sharedsorabund.o
\r
1329 # Item # 129 -- sharedsorclass --
\r
1330 ./sharedsorclass.o : sharedsorclass.cpp
\r
1331 $(CC) $(CC_OPTIONS) sharedsorclass.cpp -c $(INCLUDE) -o ./sharedsorclass.o
\r
1334 # Item # 130 -- sharedsorest --
\r
1335 ./sharedsorest.o : sharedsorest.cpp
\r
1336 $(CC) $(CC_OPTIONS) sharedsorest.cpp -c $(INCLUDE) -o ./sharedsorest.o
\r
1339 # Item # 131 -- sharedthetan --
\r
1340 ./sharedthetan.o : sharedthetan.cpp
\r
1341 $(CC) $(CC_OPTIONS) sharedthetan.cpp -c $(INCLUDE) -o ./sharedthetan.o
\r
1344 # Item # 132 -- sharedthetayc --
\r
1345 ./sharedthetayc.o : sharedthetayc.cpp
\r
1346 $(CC) $(CC_OPTIONS) sharedthetayc.cpp -c $(INCLUDE) -o ./sharedthetayc.o
\r
1349 # Item # 133 -- simpson --
\r
1350 ./simpson.o : simpson.cpp
\r
1351 $(CC) $(CC_OPTIONS) simpson.cpp -c $(INCLUDE) -o ./simpson.o
\r
1354 # Item # 134 -- singlelinkage --
\r
1355 ./singlelinkage.o : singlelinkage.cpp
\r
1356 $(CC) $(CC_OPTIONS) singlelinkage.cpp -c $(INCLUDE) -o ./singlelinkage.o
\r
1359 # Item # 135 -- sparsematrix --
\r
1360 ./sparsematrix.o : sparsematrix.cpp
\r
1361 $(CC) $(CC_OPTIONS) sparsematrix.cpp -c $(INCLUDE) -o ./sparsematrix.o
\r
1364 # Item # 136 -- summarycommand --
\r
1365 ./summarycommand.o : summarycommand.cpp
\r
1366 $(CC) $(CC_OPTIONS) summarycommand.cpp -c $(INCLUDE) -o ./summarycommand.o
\r
1369 # Item # 137 -- summarysharedcommand --
\r
1370 ./summarysharedcommand.o : summarysharedcommand.cpp
\r
1371 $(CC) $(CC_OPTIONS) summarysharedcommand.cpp -c $(INCLUDE) -o ./summarysharedcommand.o
\r
1374 # Item # 138 -- uvest --
\r
1375 ./uvest.o : uvest.cpp
\r
1376 $(CC) $(CC_OPTIONS) uvest.cpp -c $(INCLUDE) -o ./uvest.o
\r
1379 # Item # 139 -- validcalculator --
\r
1380 ./validcalculator.o : validcalculator.cpp
\r
1381 $(CC) $(CC_OPTIONS) validcalculator.cpp -c $(INCLUDE) -o ./validcalculator.o
\r
1384 # Item # 140 -- validparameter --
\r
1385 ./validparameter.o : validparameter.cpp
\r
1386 $(CC) $(CC_OPTIONS) validparameter.cpp -c $(INCLUDE) -o ./validparameter.o
\r
1389 # Item # 141 -- treenode --
\r
1390 ./treenode.o : treenode.cpp
\r
1391 $(CC) $(CC_OPTIONS) treenode.cpp -c $(INCLUDE) -o ./treenode.o
\r
1394 # Item # 142 -- readtreecommand --
\r
1395 ./readtreecommand.o : readtreecommand.cpp
\r
1396 $(CC) $(CC_OPTIONS) readtreecommand.cpp -c $(INCLUDE) -o ./readtreecommand.o
\r
1399 # Item # 143 -- reversecommand --
\r
1400 ./reversecommand.o : reversecommand.cpp
\r
1401 $(CC) $(CC_OPTIONS) reversecommand.cpp -c $(INCLUDE) -o ./reversecommand.o
\r
1404 # Item # 144 -- trimseqscommand --
\r
1405 ./trimseqscommand.o : trimseqscommand.cpp
\r
1406 $(CC) $(CC_OPTIONS) trimseqscommand.cpp -c $(INCLUDE) -o ./trimseqscommand.o
\r
1409 # Item # 145 -- slibshuff --
\r
1410 ./slibshuff.o : slibshuff.cpp
\r
1411 $(CC) $(CC_OPTIONS) slibshuff.cpp -c $(INCLUDE) -o ./slibshuff.o
\r
1414 # Item # 146 -- libshuff --
\r
1415 ./libshuff.o : libshuff.cpp
\r
1416 $(CC) $(CC_OPTIONS) libshuff.cpp -c $(INCLUDE) -o ./libshuff.o
\r
1419 # Item # 147 -- dlibshuff --
\r
1420 ./dlibshuff.o : dlibshuff.cpp
\r
1421 $(CC) $(CC_OPTIONS) dlibshuff.cpp -c $(INCLUDE) -o ./dlibshuff.o
\r
1424 # Item # 148 -- mergefilecommand --
\r
1425 ./mergefilecommand.o : mergefilecommand.cpp
\r
1426 $(CC) $(CC_OPTIONS) mergefilecommand.cpp -c $(INCLUDE) -o ./mergefilecommand.o
\r
1429 # Item # 149 -- coverage --
\r
1430 ./coverage.o : coverage.cpp
\r
1431 $(CC) $(CC_OPTIONS) coverage.cpp -c $(INCLUDE) -o ./coverage.o
\r
1434 # Item # 150 -- whittaker --
\r
1435 ./whittaker.o : whittaker.cpp
\r
1436 $(CC) $(CC_OPTIONS) whittaker.cpp -c $(INCLUDE) -o ./whittaker.o
\r
1439 # Item # 151 -- preclustercommand --
\r
1440 ./preclustercommand.o : preclustercommand.cpp
\r
1441 $(CC) $(CC_OPTIONS) preclustercommand.cpp -c $(INCLUDE) -o ./preclustercommand.o
\r
1444 # Item # 152 -- otuhierarchycommand --
\r
1445 ./otuhierarchycommand.o : otuhierarchycommand.cpp
\r
1446 $(CC) $(CC_OPTIONS) otuhierarchycommand.cpp -c $(INCLUDE) -o ./otuhierarchycommand.o
\r
1449 # Item # 153 -- setdircommand --
\r
1450 ./setdircommand.o : setdircommand.cpp
\r
1451 $(CC) $(CC_OPTIONS) setdircommand.cpp -c $(INCLUDE) -o ./setdircommand.o
\r
1454 # Item # 154 -- getgroupcommand --
\r
1455 ./getgroupcommand.o : getgroupcommand.cpp
\r
1456 $(CC) $(CC_OPTIONS) getgroupcommand.cpp -c $(INCLUDE) -o ./getgroupcommand.o
\r
1459 # Item # 155 -- getlabelcommand --
\r
1460 ./getlabelcommand.o : getlabelcommand.cpp
\r
1461 $(CC) $(CC_OPTIONS) getlabelcommand.cpp -c $(INCLUDE) -o ./getlabelcommand.o
\r
1464 # Item # 156 -- secondarystructurecommand --
\r
1465 ./secondarystructurecommand.o : secondarystructurecommand.cpp
\r
1466 $(CC) $(CC_OPTIONS) secondarystructurecommand.cpp -c $(INCLUDE) -o ./secondarystructurecommand.o
\r
1469 # Item # 157 -- mothurout --
\r
1470 ./mothurout.o : mothurout.cpp
\r
1471 $(CC) $(CC_OPTIONS) mothurout.cpp -c $(INCLUDE) -o ./mothurout.o
\r
1474 # Item # 158 -- parselistscommand --
\r
1475 ./parselistscommand.o : parselistscommand.cpp
\r
1476 $(CC) $(CC_OPTIONS) parselistscommand.cpp -c $(INCLUDE) -o ./parselistscommand.o
\r
1479 # Item # 159 -- readblast --
\r
1480 ./readblast.o : readblast.cpp
\r
1481 $(CC) $(CC_OPTIONS) readblast.cpp -c $(INCLUDE) -o ./readblast.o
\r
1484 # Item # 160 -- chimeracheckrdp --
\r
1485 ./chimeracheckrdp.o : chimeracheckrdp.cpp
\r
1486 $(CC) $(CC_OPTIONS) chimeracheckrdp.cpp -c $(INCLUDE) -o ./chimeracheckrdp.o
\r
1489 # Item # 161 -- hclustercommand --
\r
1490 ./hclustercommand.o : hclustercommand.cpp
\r
1491 $(CC) $(CC_OPTIONS) hclustercommand.cpp -c $(INCLUDE) -o ./hclustercommand.o
\r
1494 # Item # 162 -- hcluster --
\r
1495 ./hcluster.o : hcluster.cpp
\r
1496 $(CC) $(CC_OPTIONS) hcluster.cpp -c $(INCLUDE) -o ./hcluster.o
\r
1499 # Item # 163 -- getlistcountcommand --
\r
1500 ./getlistcountcommand.o : getlistcountcommand.cpp
\r
1501 $(CC) $(CC_OPTIONS) getlistcountcommand.cpp -c $(INCLUDE) -o ./getlistcountcommand.o
\r
1504 # Item # 164 -- readcluster --
\r
1505 ./readcluster.o : readcluster.cpp
\r
1506 $(CC) $(CC_OPTIONS) readcluster.cpp -c $(INCLUDE) -o ./readcluster.o
\r
1509 # Item # 165 -- ccode --
\r
1510 ./ccode.o : ccode.cpp
\r
1511 $(CC) $(CC_OPTIONS) ccode.cpp -c $(INCLUDE) -o ./ccode.o
\r
1514 # Item # 166 -- taxonomyequalizer --
\r
1515 ./taxonomyequalizer.o : taxonomyequalizer.cpp
\r
1516 $(CC) $(CC_OPTIONS) taxonomyequalizer.cpp -c $(INCLUDE) -o ./taxonomyequalizer.o
\r
1519 # Item # 167 -- phylotypecommand --
\r
1520 ./phylotypecommand.o : phylotypecommand.cpp
\r
1521 $(CC) $(CC_OPTIONS) phylotypecommand.cpp -c $(INCLUDE) -o ./phylotypecommand.o
\r
1524 # Item # 168 -- classifyseqscommand --
\r
1525 ./classifyseqscommand.o : classifyseqscommand.cpp
\r
1526 $(CC) $(CC_OPTIONS) classifyseqscommand.cpp -c $(INCLUDE) -o ./classifyseqscommand.o
\r
1529 # Item # 169 -- classify --
\r
1530 ./classify.o : classify.cpp
\r
1531 $(CC) $(CC_OPTIONS) classify.cpp -c $(INCLUDE) -o ./classify.o
\r
1534 # Item # 170 -- phylotree --
\r
1535 ./phylotree.o : phylotree.cpp
\r
1536 $(CC) $(CC_OPTIONS) phylotree.cpp -c $(INCLUDE) -o ./phylotree.o
\r
1539 # Item # 171 -- bayesian --
\r
1540 ./bayesian.o : bayesian.cpp
\r
1541 $(CC) $(CC_OPTIONS) bayesian.cpp -c $(INCLUDE) -o ./bayesian.o
\r
1544 # Item # 172 -- alignmentdb --
\r
1545 ./alignmentdb.o : alignmentdb.cpp
\r
1546 $(CC) $(CC_OPTIONS) alignmentdb.cpp -c $(INCLUDE) -o ./alignmentdb.o
\r
1549 # Item # 173 -- knn --
\r
1551 $(CC) $(CC_OPTIONS) knn.cpp -c $(INCLUDE) -o ./knn.o
\r
1554 # Item # 174 -- distancedb --
\r
1555 ./distancedb.o : distancedb.cpp
\r
1556 $(CC) $(CC_OPTIONS) distancedb.cpp -c $(INCLUDE) -o ./distancedb.o
\r
1559 # Item # 175 -- chimeraslayer --
\r
1560 ./chimeraslayer.o : chimeraslayer.cpp
\r
1561 $(CC) $(CC_OPTIONS) chimeraslayer.cpp -c $(INCLUDE) -o ./chimeraslayer.o
\r
1564 # Item # 176 -- slayer --
\r
1565 ./slayer.o : slayer.cpp
\r
1566 $(CC) $(CC_OPTIONS) slayer.cpp -c $(INCLUDE) -o ./slayer.o
\r
1569 # Item # 177 -- pcacommand --
\r
1570 ./pcacommand.o : pcacommand.cpp
\r
1571 $(CC) $(CC_OPTIONS) pcacommand.cpp -c $(INCLUDE) -o ./pcacommand.o
\r
1574 # Item # 178 -- formatcolumn --
\r
1575 ./formatcolumn.o : formatcolumn.cpp
\r
1576 $(CC) $(CC_OPTIONS) formatcolumn.cpp -c $(INCLUDE) -o ./formatcolumn.o
\r
1579 # Item # 179 -- formatphylip --
\r
1580 ./formatphylip.o : formatphylip.cpp
\r
1581 $(CC) $(CC_OPTIONS) formatphylip.cpp -c $(INCLUDE) -o ./formatphylip.o
\r
1584 # Item # 180 -- mgclustercommand --
\r
1585 ./mgclustercommand.o : mgclustercommand.cpp
\r
1586 $(CC) $(CC_OPTIONS) mgclustercommand.cpp -c $(INCLUDE) -o ./mgclustercommand.o
\r
1589 # Item # 181 -- getsharedotucommand --
\r
1590 ./getsharedotucommand.o : getsharedotucommand.cpp
\r
1591 $(CC) $(CC_OPTIONS) getsharedotucommand.cpp -c $(INCLUDE) -o ./getsharedotucommand.o
\r
1594 # Item # 182 -- maligner --
\r
1595 ./maligner.o : maligner.cpp
\r
1596 $(CC) $(CC_OPTIONS) maligner.cpp -c $(INCLUDE) -o ./maligner.o
\r
1599 # Item # 183 -- chimerarealigner --
\r
1600 ./chimerarealigner.o : chimerarealigner.cpp
\r
1601 $(CC) $(CC_OPTIONS) chimerarealigner.cpp -c $(INCLUDE) -o ./chimerarealigner.o
\r
1604 # Item # 184 -- bergerparker --
\r
1605 ./bergerparker.o : bergerparker.cpp
\r
1606 $(CC) $(CC_OPTIONS) bergerparker.cpp -c $(INCLUDE) -o ./bergerparker.o
\r
1609 # Item # 185 -- bstick --
\r
1610 ./bstick.o : bstick.cpp
\r
1611 $(CC) $(CC_OPTIONS) bstick.cpp -c $(INCLUDE) -o ./bstick.o
\r
1614 # Item # 186 -- sharedkstest --
\r
1615 ./sharedkstest.o : sharedkstest.cpp
\r
1616 $(CC) $(CC_OPTIONS) sharedkstest.cpp -c $(INCLUDE) -o ./sharedkstest.o
\r
1619 # Item # 187 -- qstat --
\r
1620 ./qstat.o : qstat.cpp
\r
1621 $(CC) $(CC_OPTIONS) qstat.cpp -c $(INCLUDE) -o ./qstat.o
\r
1624 # Item # 188 -- shen --
\r
1625 ./shen.o : shen.cpp
\r
1626 $(CC) $(CC_OPTIONS) shen.cpp -c $(INCLUDE) -o ./shen.o
\r
1629 # Item # 189 -- logsd --
\r
1630 ./logsd.o : logsd.cpp
\r
1631 $(CC) $(CC_OPTIONS) logsd.cpp -c $(INCLUDE) -o ./logsd.o
\r
1634 # Item # 190 -- geom --
\r
1635 ./geom.o : geom.cpp
\r
1636 $(CC) $(CC_OPTIONS) geom.cpp -c $(INCLUDE) -o ./geom.o
\r
1638 # Item # 191 -- parsesffcommand --
\r
1639 ./parsesffcommand.o : parsesffcommand.cpp
\r
1640 $(CC) $(CC_OPTIONS) parsesffcommand.cpp -c $(INCLUDE) -o ./parsesffcommand.o
\r
1642 # Item # 192 -- chimeraccodecommand --
\r
1643 ./chimeraccodecommand.o : chimeraccodecommand.cpp
\r
1644 $(CC) $(CC_OPTIONS) chimeraccodecommand.cpp -c $(INCLUDE) -o ./chimeraccodecommand.o
\r
1646 # Item # 193 -- chimeracheckcommand --
\r
1647 ./chimeracheckcommand.o : chimeracheckcommand.cpp
\r
1648 $(CC) $(CC_OPTIONS) chimeracheckcommand.cpp -c $(INCLUDE) -o ./chimeracheckcommand.o
\r
1651 # Item # 194 -- chimeraslayercommand --
\r
1652 ./chimeraslayercommand.o : chimeraslayercommand.cpp
\r
1653 $(CC) $(CC_OPTIONS) chimeraslayercommand.cpp -c $(INCLUDE) -o ./chimeraslayercommand.o
\r
1655 # Item # 195 -- chimerapintailcommand --
\r
1656 ./chimerapintailcommand.o : chimerapintailcommand.cpp
\r
1657 $(CC) $(CC_OPTIONS) chimerapintailcommand.cpp -c $(INCLUDE) -o ./chimerapintailcommand.o
\r
1659 # Item # 196 -- chimerabellerophoncommand --
\r
1660 ./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp
\r
1661 $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o
\r
1663 # Item # 197 -- phylosummary --
\r
1664 ./phylosummary.o : phylosummary.cpp
\r
1665 $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o
\r
1667 # Item # 198 -- setlogfilecommand --
\r
1668 ./setlogfilecommand.o : setlogfilecommand.cpp
\r
1669 $(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o
\r
1671 # Item # 199 -- phylodiversity --
\r
1672 ./phylodiversity.o : phylodiversity.cpp
\r
1673 $(CC) $(CC_OPTIONS) phylodiversity.cpp -c $(INCLUDE) -o ./phylodiversity.o
\r
1675 # Item # 200 -- phylodiversitycommand --
\r
1676 ./phylodiversitycommand.o : phylodiversitycommand.cpp
\r
1677 $(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o
\r
1679 # Item # 201 -- makegroupcommand --
\r
1680 ./makegroupcommand.o : makegroupcommand.cpp
\r
1681 $(CC) $(CC_OPTIONS) makegroupcommand.cpp -c $(INCLUDE) -o ./makegroupcommand.o
\r
1683 # Item # 202 -- chopseqscommand --
\r
1684 ./chopseqscommand.o : chopseqscommand.cpp
\r
1685 $(CC) $(CC_OPTIONS) chopseqscommand.cpp -c $(INCLUDE) -o ./chopseqscommand.o
\r
1687 # Item # 203 -- clearcutcommand --
\r
1688 ./clearcutcommand.o : clearcutcommand.cpp
\r
1689 $(CC) $(CC_OPTIONS) clearcutcommand.cpp -c $(INCLUDE) -o ./clearcutcommand.o
\r
1691 # Item # 204 -- catchallcommand --
\r
1692 ./catchallcommand.o : catchallcommand.cpp
\r
1693 $(CC) $(CC_OPTIONS) catchallcommand.cpp -c $(INCLUDE) -o ./catchallcommand.o
\r
1695 # Item # 205 -- splitabundcommand --
\r
1696 ./splitabundcommand.o : splitabundcommand.cpp
\r
1697 $(CC) $(CC_OPTIONS) splitabundcommand.cpp -c $(INCLUDE) -o ./splitabundcommand.o
\r
1699 # Item # 206 -- splitmatrix --
\r
1700 ./splitmatrix.o : splitmatrix.cpp
\r
1701 $(CC) $(CC_OPTIONS) splitmatrix.cpp -c $(INCLUDE) -o ./splitmatrix.o
\r
1703 # Item # 207 -- clustersplit --
\r
1704 ./clustersplitcommand.o : clustersplitcommand.cpp
\r
1705 $(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o
\r
1707 # Item # 208 -- classifyotu --
\r
1708 ./classifyotucommand.o : classifyotucommand.cpp
\r
1709 $(CC) $(CC_OPTIONS) classifyotucommand.cpp -c $(INCLUDE) -o ./classifyotucommand.o
\r
1711 # Item # 209 -- weightedlinkage --
\r
1712 ./weightedlinkage.o : weightedlinkage.cpp
\r
1713 $(CC) $(CC_OPTIONS) weightedlinkage.cpp -c $(INCLUDE) -o ./weightedlinkage.o
\r
1715 ##### END RUN ####
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