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\
\r
126 ./removeseqscommand.o\
\r
128 ./binsequencecommand.o\
\r
129 ./distancecommand.o\
\r
131 ./averagelinkage.o\
\r
136 ./clustercommand.o\
\r
138 ./collectcommand.o\
\r
139 ./collectsharedcommand.o\
\r
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
162 ./nameassignment.o\
\r
171 ./rarefactcommand.o\
\r
172 ./rarefactsharedcommand.o\
\r
182 ./sharedordervector.o\
\r
183 ./sharedrabundvector.o\
\r
184 ./sharedsabundvector.o\
\r
186 ./sharedsorabund.o\
\r
187 ./sharedsorclass.o\
\r
194 ./summarycommand.o\
\r
195 ./summarysharedcommand.o\
\r
197 ./validcalculator.o\
\r
198 ./validparameter.o\
\r
200 ./readtreecommand.o\
\r
201 ./reversecommand.o\
\r
202 ./trimseqscommand.o\
\r
206 ./mergefilecommand.o\
\r
209 ./preclustercommand.o\
\r
210 ./otuhierarchycommand.o\
\r
212 ./getgroupcommand.o\
\r
213 ./getlabelcommand.o\
\r
214 ./secondarystructurecommand.o\
\r
216 ./parselistscommand.o\
\r
218 ./chimeracheckrdp.o\
\r
219 ./hclustercommand.o\
\r
221 ./getlistcountcommand.o\
\r
224 ./taxonomyequalizer.o\
\r
225 ./phylotypecommand.o\
\r
226 ./classifyseqscommand.o\
\r
227 ./classifyotucommand.o\
\r
228 ./parsesffcommand.o\
\r
231 ./phylodiversity.o\
\r
232 ./phylodiversitycommand.o\
\r
243 ./mgclustercommand.o\
\r
244 ./getsharedotucommand.o\
\r
246 ./chimerarealigner.o\
\r
254 ./setlogfilecommand.o
\r
255 $(CC) $(LNK_OPTIONS) \
\r
256 ./sharedutilities.o\
\r
257 ./treegroupscommand.o\
\r
258 ./bootstrapsharedcommand.o\
\r
259 ./matrixoutputcommand.o\
\r
260 ./getoturepcommand.o\
\r
261 ./screenseqscommand.o\
\r
264 ./readotucommand.o\
\r
265 ./readdistcommand.o\
\r
266 ./commandfactory.o\
\r
271 ./needlemanoverlap.o\
\r
283 ./unifracweightedcommand.o\
\r
286 ./unifracunweightedcommand.o\
\r
287 ./getsabundcommand.o\
\r
288 ./getrabundcommand.o\
\r
291 ./sharedanderbergs.o\
\r
296 ./heatmapcommand.o\
\r
297 ./libshuffcommand.o\
\r
299 ./sharedbraycurtis.o\
\r
300 ./sharedkulczynski.o\
\r
302 ./sharedkulczynskicody.o\
\r
303 ./sharedmorisitahorn.o\
\r
308 ./consensuscommand.o\
\r
309 ./heatmapsimcommand.o\
\r
312 ./filterseqscommand.o\
\r
315 ./sharedjackknife.o\
\r
316 ./sharedmarczewski.o\
\r
319 ./parsimonycommand.o\
\r
321 ./seqsummarycommand.o\
\r
322 ./chimeraccodecommand.o\
\r
323 ./chimerabellerophoncommand.o\
\r
324 ./chimeracheckcommand.o\
\r
325 ./chimeraslayercommand.o\
\r
326 ./chimerapintailcommand.o\
\r
327 ./chimeraseqscommand.o\
\r
328 ./sharedlistvector.o\
\r
331 ./sharedsobscollectsummary.o\
\r
332 ./deconvolutecommand.o\
\r
333 ./listseqscommand.o\
\r
334 ./getseqscommand.o\
\r
335 ./removeseqscommand.o\
\r
337 ./binsequencecommand.o\
\r
338 ./distancecommand.o\
\r
340 ./averagelinkage.o\
\r
345 ./clustercommand.o\
\r
347 ./collectcommand.o\
\r
348 ./collectsharedcommand.o\
\r
349 ./commandoptionparser.o\
\r
350 ./completelinkage.o\
\r
358 ./makegroupcommand.o\
\r
359 ./chopseqscommand.o\
\r
360 ./clearcutcommand.o\
\r
361 ./catchallcommand.o\
\r
362 ./splitabundcommand.o\
\r
364 ./clustersplitcommand.o\
\r
371 ./nameassignment.o\
\r
380 ./rarefactcommand.o\
\r
381 ./rarefactsharedcommand.o\
\r
391 ./sharedordervector.o\
\r
392 ./sharedrabundvector.o\
\r
393 ./sharedsabundvector.o\
\r
395 ./sharedsorabund.o\
\r
396 ./sharedsorclass.o\
\r
403 ./summarycommand.o\
\r
404 ./summarysharedcommand.o\
\r
406 ./validcalculator.o\
\r
407 ./validparameter.o\
\r
409 ./readtreecommand.o\
\r
410 ./reversecommand.o\
\r
411 ./trimseqscommand.o\
\r
415 ./mergefilecommand.o\
\r
418 ./preclustercommand.o\
\r
419 ./otuhierarchycommand.o\
\r
421 ./getgroupcommand.o\
\r
422 ./getlabelcommand.o\
\r
423 ./secondarystructurecommand.o\
\r
425 ./parselistscommand.o\
\r
427 ./chimeracheckrdp.o\
\r
428 ./hclustercommand.o\
\r
430 ./getlistcountcommand.o\
\r
433 ./taxonomyequalizer.o\
\r
434 ./phylotypecommand.o\
\r
435 ./classifyseqscommand.o\
\r
436 ./classifyotucommand.o\
\r
437 ./parsesffcommand.o\
\r
440 ./phylodiversity.o\
\r
441 ./phylodiversitycommand.o\
\r
452 ./mgclustercommand.o\
\r
453 ./getsharedotucommand.o\
\r
455 ./chimerarealigner.o\
\r
463 ./setlogfilecommand.o\
\r
464 -o ../Release/mothur
\r
468 ./sharedutilities.o\
\r
469 ./treegroupscommand.o\
\r
470 ./bootstrapsharedcommand.o\
\r
471 ./matrixoutputcommand.o\
\r
472 ./getoturepcommand.o\
\r
473 ./screenseqscommand.o\
\r
476 ./readotucommand.o\
\r
477 ./readdistcommand.o\
\r
478 ./commandfactory.o\
\r
483 ./needlemanoverlap.o\
\r
495 ./unifracweightedcommand.o\
\r
498 ./unifracunweightedcommand.o\
\r
499 ./getsabundcommand.o\
\r
500 ./getrabundcommand.o\
\r
503 ./sharedanderbergs.o\
\r
508 ./heatmapcommand.o\
\r
509 ./libshuffcommand.o\
\r
511 ./sharedbraycurtis.o\
\r
512 ./sharedkulczynski.o\
\r
514 ./sharedkulczynskicody.o\
\r
515 ./sharedmorisitahorn.o\
\r
520 ./consensuscommand.o\
\r
521 ./heatmapsimcommand.o\
\r
524 ./filterseqscommand.o\
\r
527 ./sharedjackknife.o\
\r
528 ./sharedmarczewski.o\
\r
531 ./parsimonycommand.o\
\r
533 ./seqsummarycommand.o\
\r
534 ./chimeraccodecommand.o\
\r
535 ./chimerabellerophoncommand.o\
\r
536 ./chimeracheckcommand.o\
\r
537 ./chimeraslayercommand.o\
\r
538 ./chimerapintailcommand.o\
\r
539 ./chimeraseqscommand.o\
\r
540 ./sharedlistvector.o\
\r
543 ./sharedsobscollectsummary.o\
\r
544 ./deconvolutecommand.o\
\r
545 ./listseqscommand.o\
\r
546 ./getseqscommand.o\
\r
547 ./removeseqscommand.o\
\r
549 ./binsequencecommand.o\
\r
550 ./distancecommand.o\
\r
552 ./averagelinkage.o\
\r
557 ./clustercommand.o\
\r
559 ./collectcommand.o\
\r
560 ./collectsharedcommand.o\
\r
561 ./commandoptionparser.o\
\r
562 ./completelinkage.o\
\r
570 ./makegroupcommand.o\
\r
571 ./chopseqscommand.o\
\r
572 ./clearcutcommand.o\
\r
573 ./catchallcommand.o\
\r
574 ./splitabundcommand.o\
\r
576 ./clustersplitcommand.o\
\r
583 ./nameassignment.o\
\r
592 ./rarefactcommand.o\
\r
593 ./rarefactsharedcommand.o\
\r
603 ./sharedordervector.o\
\r
604 ./sharedrabundvector.o\
\r
605 ./sharedsabundvector.o\
\r
607 ./sharedsorabund.o\
\r
608 ./sharedsorclass.o\
\r
615 ./summarycommand.o\
\r
616 ./summarysharedcommand.o\
\r
618 ./validcalculator.o\
\r
619 ./validparameter.o\
\r
621 ./readtreecommand.o\
\r
622 ./reversecommand.o\
\r
623 ./trimseqscommand.o\
\r
627 ./mergefilecommand.o\
\r
630 ./preclustercommand.o\
\r
631 ./otuhierarchycommand.o\
\r
633 ./getgroupcommand.o\
\r
634 ./getlabelcommand.o\
\r
635 ./secondarystructurecommand.o\
\r
637 ./parselistscommand.o\
\r
639 ./chimeracheckrdp.o\
\r
640 ./hclustercommand.o\
\r
642 ./getlistcountcommand.o\
\r
645 ./taxonomyequalizer.o\
\r
646 ./phylotypecommand.o\
\r
647 ./classifyseqscommand.o\
\r
648 ./classifyotucommand.o\
\r
649 ./parsesffcommand.o\
\r
652 ./phylodiversity.o\
\r
653 ./phylodiversitycommand.o\
\r
664 ./mgclustercommand.o\
\r
665 ./getsharedotucommand.o\
\r
667 ./chimerarealigner.o\
\r
675 ./setlogfilecommand.o\
\r
679 #cp mothur ../Release/mothur
\r
682 # Build the parts of mothur
\r
686 # Item # 1 -- sharedutilities --
\r
687 ./sharedutilities.o : sharedutilities.cpp
\r
688 $(CC) $(CC_OPTIONS) sharedutilities.cpp -c $(INCLUDE) -o ./sharedutilities.o
\r
691 # Item # 2 -- treegroupscommand --
\r
692 ./treegroupscommand.o : treegroupscommand.cpp
\r
693 $(CC) $(CC_OPTIONS) treegroupscommand.cpp -c $(INCLUDE) -o ./treegroupscommand.o
\r
696 # Item # 3 -- bootstrapsharedcommand --
\r
697 ./bootstrapsharedcommand.o : bootstrapsharedcommand.cpp
\r
698 $(CC) $(CC_OPTIONS) bootstrapsharedcommand.cpp -c $(INCLUDE) -o ./bootstrapsharedcommand.o
\r
701 # Item # 4 -- matrixoutputcommand --
\r
702 ./matrixoutputcommand.o : matrixoutputcommand.cpp
\r
703 $(CC) $(CC_OPTIONS) matrixoutputcommand.cpp -c $(INCLUDE) -o ./matrixoutputcommand.o
\r
706 # Item # 5 -- getoturepcommand --
\r
707 ./getoturepcommand.o : getoturepcommand.cpp
\r
708 $(CC) $(CC_OPTIONS) getoturepcommand.cpp -c $(INCLUDE) -o ./getoturepcommand.o
\r
711 # Item # 6 -- screenseqscommand --
\r
712 ./screenseqscommand.o : screenseqscommand.cpp
\r
713 $(CC) $(CC_OPTIONS) screenseqscommand.cpp -c $(INCLUDE) -o ./screenseqscommand.o
\r
716 # Item # 7 -- chimera --
\r
717 ./chimera.o : chimera.cpp
\r
718 $(CC) $(CC_OPTIONS) chimera.cpp -c $(INCLUDE) -o ./chimera.o
\r
721 # Item # 8 -- decalc --
\r
722 ./decalc.o : decalc.cpp
\r
723 $(CC) $(CC_OPTIONS) decalc.cpp -c $(INCLUDE) -o ./decalc.o
\r
726 # Item # 9 -- readotucommand --
\r
727 ./readotucommand.o : readotucommand.cpp
\r
728 $(CC) $(CC_OPTIONS) readotucommand.cpp -c $(INCLUDE) -o ./readotucommand.o
\r
731 # Item # 10 -- readdistcommand --
\r
732 ./readdistcommand.o : readdistcommand.cpp
\r
733 $(CC) $(CC_OPTIONS) readdistcommand.cpp -c $(INCLUDE) -o ./readdistcommand.o
\r
736 # Item # 11 -- commandfactory --
\r
737 ./commandfactory.o : commandfactory.cpp
\r
738 $(CC) $(CC_OPTIONS) commandfactory.cpp -c $(INCLUDE) -o ./commandfactory.o
\r
741 # Item # 12 -- alignment --
\r
742 ./alignment.o : alignment.cpp
\r
743 $(CC) $(CC_OPTIONS) alignment.cpp -c $(INCLUDE) -o ./alignment.o
\r
746 # Item # 13 -- alignmentcell --
\r
747 ./alignmentcell.o : alignmentcell.cpp
\r
748 $(CC) $(CC_OPTIONS) alignmentcell.cpp -c $(INCLUDE) -o ./alignmentcell.o
\r
751 # Item # 14 -- gotohoverlap --
\r
752 ./gotohoverlap.o : gotohoverlap.cpp
\r
753 $(CC) $(CC_OPTIONS) gotohoverlap.cpp -c $(INCLUDE) -o ./gotohoverlap.o
\r
756 # Item # 15 -- overlap --
\r
757 ./overlap.o : overlap.cpp
\r
758 $(CC) $(CC_OPTIONS) overlap.cpp -c $(INCLUDE) -o ./overlap.o
\r
761 # Item # 16 -- needlemanoverlap --
\r
762 ./needlemanoverlap.o : needlemanoverlap.cpp
\r
763 $(CC) $(CC_OPTIONS) needlemanoverlap.cpp -c $(INCLUDE) -o ./needlemanoverlap.o
\r
766 # Item # 17 -- blastalign --
\r
767 ./blastalign.o : blastalign.cpp
\r
768 $(CC) $(CC_OPTIONS) blastalign.cpp -c $(INCLUDE) -o ./blastalign.o
\r
771 # Item # 18 -- noalign --
\r
772 ./noalign.o : noalign.cpp
\r
773 $(CC) $(CC_OPTIONS) noalign.cpp -c $(INCLUDE) -o ./noalign.o
\r
776 # Item # 19 -- suffixdb --
\r
777 ./suffixdb.o : suffixdb.cpp
\r
778 $(CC) $(CC_OPTIONS) suffixdb.cpp -c $(INCLUDE) -o ./suffixdb.o
\r
781 # Item # 20 -- suffixnodes --
\r
782 ./suffixnodes.o : suffixnodes.cpp
\r
783 $(CC) $(CC_OPTIONS) suffixnodes.cpp -c $(INCLUDE) -o ./suffixnodes.o
\r
786 # Item # 21 -- suffixtree --
\r
787 ./suffixtree.o : suffixtree.cpp
\r
788 $(CC) $(CC_OPTIONS) suffixtree.cpp -c $(INCLUDE) -o ./suffixtree.o
\r
791 # Item # 22 -- blastdb --
\r
792 ./blastdb.o : blastdb.cpp
\r
793 $(CC) $(CC_OPTIONS) blastdb.cpp -c $(INCLUDE) -o ./blastdb.o
\r
796 # Item # 23 -- nast --
\r
797 ./nast.o : nast.cpp
\r
798 $(CC) $(CC_OPTIONS) nast.cpp -c $(INCLUDE) -o ./nast.o
\r
801 # Item # 24 -- nastreport --
\r
802 ./nastreport.o : nastreport.cpp
\r
803 $(CC) $(CC_OPTIONS) nastreport.cpp -c $(INCLUDE) -o ./nastreport.o
\r
806 # Item # 25 -- boneh --
\r
807 ./boneh.o : boneh.cpp
\r
808 $(CC) $(CC_OPTIONS) boneh.cpp -c $(INCLUDE) -o ./boneh.o
\r
811 # Item # 26 -- efron --
\r
812 ./efron.o : efron.cpp
\r
813 $(CC) $(CC_OPTIONS) efron.cpp -c $(INCLUDE) -o ./efron.o
\r
816 # Item # 27 -- solow --
\r
817 ./solow.o : solow.cpp
\r
818 $(CC) $(CC_OPTIONS) solow.cpp -c $(INCLUDE) -o ./solow.o
\r
821 # Item # 28 -- unifracweightedcommand --
\r
822 ./unifracweightedcommand.o : unifracweightedcommand.cpp
\r
823 $(CC) $(CC_OPTIONS) unifracweightedcommand.cpp -c $(INCLUDE) -o ./unifracweightedcommand.o
\r
826 # Item # 29 -- weighted --
\r
827 ./weighted.o : weighted.cpp
\r
828 $(CC) $(CC_OPTIONS) weighted.cpp -c $(INCLUDE) -o ./weighted.o
\r
831 # Item # 30 -- unweighted --
\r
832 ./unweighted.o : unweighted.cpp
\r
833 $(CC) $(CC_OPTIONS) unweighted.cpp -c $(INCLUDE) -o ./unweighted.o
\r
836 # Item # 31 -- unifracunweightedcommand --
\r
837 ./unifracunweightedcommand.o : unifracunweightedcommand.cpp
\r
838 $(CC) $(CC_OPTIONS) unifracunweightedcommand.cpp -c $(INCLUDE) -o ./unifracunweightedcommand.o
\r
841 # Item # 32 -- getsabundcommand --
\r
842 ./getsabundcommand.o : getsabundcommand.cpp
\r
843 $(CC) $(CC_OPTIONS) getsabundcommand.cpp -c $(INCLUDE) -o ./getsabundcommand.o
\r
846 # Item # 33 -- getrabundcommand --
\r
847 ./getrabundcommand.o : getrabundcommand.cpp
\r
848 $(CC) $(CC_OPTIONS) getrabundcommand.cpp -c $(INCLUDE) -o ./getrabundcommand.o
\r
851 # Item # 34 -- bellerophon --
\r
852 ./bellerophon.o : bellerophon.cpp
\r
853 $(CC) $(CC_OPTIONS) bellerophon.cpp -c $(INCLUDE) -o ./bellerophon.o
\r
856 # Item # 35 -- pintail --
\r
857 ./pintail.o : pintail.cpp
\r
858 $(CC) $(CC_OPTIONS) pintail.cpp -c $(INCLUDE) -o ./pintail.o
\r
861 # Item # 36 -- sharedanderbergs --
\r
862 ./sharedanderbergs.o : sharedanderbergs.cpp
\r
863 $(CC) $(CC_OPTIONS) sharedanderbergs.cpp -c $(INCLUDE) -o ./sharedanderbergs.o
\r
866 # Item # 37 -- venncommand --
\r
867 ./venncommand.o : venncommand.cpp
\r
868 $(CC) $(CC_OPTIONS) venncommand.cpp -c $(INCLUDE) -o ./venncommand.o
\r
871 # Item # 38 -- venn --
\r
872 ./venn.o : venn.cpp
\r
873 $(CC) $(CC_OPTIONS) venn.cpp -c $(INCLUDE) -o ./venn.o
\r
876 # Item # 39 -- fullmatrix --
\r
877 ./fullmatrix.o : fullmatrix.cpp
\r
878 $(CC) $(CC_OPTIONS) fullmatrix.cpp -c $(INCLUDE) -o ./fullmatrix.o
\r
881 # Item # 40 -- heatmap --
\r
882 ./heatmap.o : heatmap.cpp
\r
883 $(CC) $(CC_OPTIONS) heatmap.cpp -c $(INCLUDE) -o ./heatmap.o
\r
886 # Item # 41 -- heatmapcommand --
\r
887 ./heatmapcommand.o : heatmapcommand.cpp
\r
888 $(CC) $(CC_OPTIONS) heatmapcommand.cpp -c $(INCLUDE) -o ./heatmapcommand.o
\r
891 # Item # 42 -- libshuffcommand --
\r
892 ./libshuffcommand.o : libshuffcommand.cpp
\r
893 $(CC) $(CC_OPTIONS) libshuffcommand.cpp -c $(INCLUDE) -o ./libshuffcommand.o
\r
896 # Item # 43 -- nocommands --
\r
897 ./nocommands.o : nocommands.cpp
\r
898 $(CC) $(CC_OPTIONS) nocommands.cpp -c $(INCLUDE) -o ./nocommands.o
\r
901 # Item # 44 -- sharedbraycurtis --
\r
902 ./sharedbraycurtis.o : sharedbraycurtis.cpp
\r
903 $(CC) $(CC_OPTIONS) sharedbraycurtis.cpp -c $(INCLUDE) -o ./sharedbraycurtis.o
\r
906 # Item # 45 -- sharedkulczynski --
\r
907 ./sharedkulczynski.o : sharedkulczynski.cpp
\r
908 $(CC) $(CC_OPTIONS) sharedkulczynski.cpp -c $(INCLUDE) -o ./sharedkulczynski.o
\r
911 # Item # 46 -- sharedlennon --
\r
912 ./sharedlennon.o : sharedlennon.cpp
\r
913 $(CC) $(CC_OPTIONS) sharedlennon.cpp -c $(INCLUDE) -o ./sharedlennon.o
\r
916 # Item # 47 -- sharedkulczynskicody --
\r
917 ./sharedkulczynskicody.o : sharedkulczynskicody.cpp
\r
918 $(CC) $(CC_OPTIONS) sharedkulczynskicody.cpp -c $(INCLUDE) -o ./sharedkulczynskicody.o
\r
921 # Item # 48 -- sharedmorisitahorn --
\r
922 ./sharedmorisitahorn.o : sharedmorisitahorn.cpp
\r
923 $(CC) $(CC_OPTIONS) sharedmorisitahorn.cpp -c $(INCLUDE) -o ./sharedmorisitahorn.o
\r
926 # Item # 49 -- sharedochiai --
\r
927 ./sharedochiai.o : sharedochiai.cpp
\r
928 $(CC) $(CC_OPTIONS) sharedochiai.cpp -c $(INCLUDE) -o ./sharedochiai.o
\r
931 # Item # 50 -- readcolumn --
\r
932 ./readcolumn.o : readcolumn.cpp
\r
933 $(CC) $(CC_OPTIONS) readcolumn.cpp -c $(INCLUDE) -o ./readcolumn.o
\r
936 # Item # 51 -- readotu --
\r
937 ./readotu.o : readotu.cpp
\r
938 $(CC) $(CC_OPTIONS) readotu.cpp -c $(INCLUDE) -o ./readotu.o
\r
941 # Item # 52 -- readphylip --
\r
942 ./readphylip.o : readphylip.cpp
\r
943 $(CC) $(CC_OPTIONS) readphylip.cpp -c $(INCLUDE) -o ./readphylip.o
\r
946 # Item # 53 -- consensuscommand --
\r
947 ./consensuscommand.o : consensuscommand.cpp
\r
948 $(CC) $(CC_OPTIONS) consensuscommand.cpp -c $(INCLUDE) -o ./consensuscommand.o
\r
951 # Item # 54 -- heatmapsimcommand --
\r
952 ./heatmapsimcommand.o : heatmapsimcommand.cpp
\r
953 $(CC) $(CC_OPTIONS) heatmapsimcommand.cpp -c $(INCLUDE) -o ./heatmapsimcommand.o
\r
956 # Item # 55 -- heatmapsim --
\r
957 ./heatmapsim.o : heatmapsim.cpp
\r
958 $(CC) $(CC_OPTIONS) heatmapsim.cpp -c $(INCLUDE) -o ./heatmapsim.o
\r
961 # Item # 56 -- optionparser --
\r
962 ./optionparser.o : optionparser.cpp
\r
963 $(CC) $(CC_OPTIONS) optionparser.cpp -c $(INCLUDE) -o ./optionparser.o
\r
966 # Item # 57 -- filterseqscommand --
\r
967 ./filterseqscommand.o : filterseqscommand.cpp
\r
968 $(CC) $(CC_OPTIONS) filterseqscommand.cpp -c $(INCLUDE) -o ./filterseqscommand.o
\r
971 # Item # 58 -- goodscoverage --
\r
972 ./goodscoverage.o : goodscoverage.cpp
\r
973 $(CC) $(CC_OPTIONS) goodscoverage.cpp -c $(INCLUDE) -o ./goodscoverage.o
\r
976 # Item # 59 -- sequencedb --
\r
977 ./sequencedb.o : sequencedb.cpp
\r
978 $(CC) $(CC_OPTIONS) sequencedb.cpp -c $(INCLUDE) -o ./sequencedb.o
\r
981 # Item # 60 -- sharedjackknife --
\r
982 ./sharedjackknife.o : sharedjackknife.cpp
\r
983 $(CC) $(CC_OPTIONS) sharedjackknife.cpp -c $(INCLUDE) -o ./sharedjackknife.o
\r
986 # Item # 61 -- sharedmarczewski --
\r
987 ./sharedmarczewski.o : sharedmarczewski.cpp
\r
988 $(CC) $(CC_OPTIONS) sharedmarczewski.cpp -c $(INCLUDE) -o ./sharedmarczewski.o
\r
991 # Item # 62 -- aligncommand --
\r
992 ./aligncommand.o : aligncommand.cpp
\r
993 $(CC) $(CC_OPTIONS) aligncommand.cpp -c $(INCLUDE) -o ./aligncommand.o
\r
996 # Item # 63 -- treemap --
\r
997 ./treemap.o : treemap.cpp
\r
998 $(CC) $(CC_OPTIONS) treemap.cpp -c $(INCLUDE) -o ./treemap.o
\r
1001 # Item # 64 -- parsimonycommand --
\r
1002 ./parsimonycommand.o : parsimonycommand.cpp
\r
1003 $(CC) $(CC_OPTIONS) parsimonycommand.cpp -c $(INCLUDE) -o ./parsimonycommand.o
\r
1006 # Item # 65 -- parsimony --
\r
1007 ./parsimony.o : parsimony.cpp
\r
1008 $(CC) $(CC_OPTIONS) parsimony.cpp -c $(INCLUDE) -o ./parsimony.o
\r
1011 # Item # 66 -- seqsummarycommand --
\r
1012 ./seqsummarycommand.o : seqsummarycommand.cpp
\r
1013 $(CC) $(CC_OPTIONS) seqsummarycommand.cpp -c $(INCLUDE) -o ./seqsummarycommand.o
\r
1016 # Item # 67 -- chimeraseqscommand --
\r
1017 ./chimeraseqscommand.o : chimeraseqscommand.cpp
\r
1018 $(CC) $(CC_OPTIONS) chimeraseqscommand.cpp -c $(INCLUDE) -o ./chimeraseqscommand.o
\r
1021 # Item # 68 -- sharedlistvector --
\r
1022 ./sharedlistvector.o : sharedlistvector.cpp
\r
1023 $(CC) $(CC_OPTIONS) sharedlistvector.cpp -c $(INCLUDE) -o ./sharedlistvector.o
\r
1026 # Item # 69 -- tree --
\r
1027 ./tree.o : tree.cpp
\r
1028 $(CC) $(CC_OPTIONS) tree.cpp -c $(INCLUDE) -o ./tree.o
\r
1031 # Item # 70 -- readtree --
\r
1032 ./readtree.o : readtree.cpp
\r
1033 $(CC) $(CC_OPTIONS) readtree.cpp -c $(INCLUDE) -o ./readtree.o
\r
1036 # Item # 71 -- sharedsobscollectsummary --
\r
1037 ./sharedsobscollectsummary.o : sharedsobscollectsummary.cpp
\r
1038 $(CC) $(CC_OPTIONS) sharedsobscollectsummary.cpp -c $(INCLUDE) -o ./sharedsobscollectsummary.o
\r
1041 # Item # 72 -- deconvolutecommand --
\r
1042 ./deconvolutecommand.o : deconvolutecommand.cpp
\r
1043 $(CC) $(CC_OPTIONS) deconvolutecommand.cpp -c $(INCLUDE) -o ./deconvolutecommand.o
\r
1046 # Item # 73 -- listseqscommand --
\r
1047 ./listseqscommand.o : listseqscommand.cpp
\r
1048 $(CC) $(CC_OPTIONS) listseqscommand.cpp -c $(INCLUDE) -o ./listseqscommand.o
\r
1051 # Item # 74 -- getseqscommand --
\r
1052 ./getseqscommand.o : getseqscommand.cpp
\r
1053 $(CC) $(CC_OPTIONS) getseqscommand.cpp -c $(INCLUDE) -o ./getseqscommand.o
\r
1056 # Item # 75 -- removeseqscommand --
\r
1057 ./removeseqscommand.o : removeseqscommand.cpp
\r
1058 $(CC) $(CC_OPTIONS) removeseqscommand.cpp -c $(INCLUDE) -o ./removeseqscommand.o
\r
1061 # Item # 76 -- systemcommand --
\r
1062 ./systemcommand.o : systemcommand.cpp
\r
1063 $(CC) $(CC_OPTIONS) systemcommand.cpp -c $(INCLUDE) -o ./systemcommand.o
\r
1066 # Item # 77 -- binsequencecommand --
\r
1067 ./binsequencecommand.o : binsequencecommand.cpp
\r
1068 $(CC) $(CC_OPTIONS) binsequencecommand.cpp -c $(INCLUDE) -o ./binsequencecommand.o
\r
1071 # Item # 78 -- distancecommand --
\r
1072 ./distancecommand.o : distancecommand.cpp
\r
1073 $(CC) $(CC_OPTIONS) distancecommand.cpp -c $(INCLUDE) -o ./distancecommand.o
\r
1076 # Item # 79 -- ace --
\r
1078 $(CC) $(CC_OPTIONS) ace.cpp -c $(INCLUDE) -o ./ace.o
\r
1081 # Item # 80 -- averagelinkage --
\r
1082 ./averagelinkage.o : averagelinkage.cpp
\r
1083 $(CC) $(CC_OPTIONS) averagelinkage.cpp -c $(INCLUDE) -o ./averagelinkage.o
\r
1086 # Item # 81 -- bootstrap --
\r
1087 ./bootstrap.o : bootstrap.cpp
\r
1088 $(CC) $(CC_OPTIONS) bootstrap.cpp -c $(INCLUDE) -o ./bootstrap.o
\r
1091 # Item # 82 -- calculator --
\r
1092 ./calculator.o : calculator.cpp
\r
1093 $(CC) $(CC_OPTIONS) calculator.cpp -c $(INCLUDE) -o ./calculator.o
\r
1096 # Item # 83 -- chao1 --
\r
1097 ./chao1.o : chao1.cpp
\r
1098 $(CC) $(CC_OPTIONS) chao1.cpp -c $(INCLUDE) -o ./chao1.o
\r
1101 # Item # 84 -- cluster --
\r
1102 ./cluster.o : cluster.cpp
\r
1103 $(CC) $(CC_OPTIONS) cluster.cpp -c $(INCLUDE) -o ./cluster.o
\r
1106 # Item # 85 -- clustercommand --
\r
1107 ./clustercommand.o : clustercommand.cpp
\r
1108 $(CC) $(CC_OPTIONS) clustercommand.cpp -c $(INCLUDE) -o ./clustercommand.o
\r
1111 # Item # 86 -- collect --
\r
1112 ./collect.o : collect.cpp
\r
1113 $(CC) $(CC_OPTIONS) collect.cpp -c $(INCLUDE) -o ./collect.o
\r
1116 # Item # 87 -- collectcommand --
\r
1117 ./collectcommand.o : collectcommand.cpp
\r
1118 $(CC) $(CC_OPTIONS) collectcommand.cpp -c $(INCLUDE) -o ./collectcommand.o
\r
1121 # Item # 88 -- collectsharedcommand --
\r
1122 ./collectsharedcommand.o : collectsharedcommand.cpp
\r
1123 $(CC) $(CC_OPTIONS) collectsharedcommand.cpp -c $(INCLUDE) -o ./collectsharedcommand.o
\r
1126 # Item # 89 -- commandoptionparser --
\r
1127 ./commandoptionparser.o : commandoptionparser.cpp
\r
1128 $(CC) $(CC_OPTIONS) commandoptionparser.cpp -c $(INCLUDE) -o ./commandoptionparser.o
\r
1131 # Item # 90 -- completelinkage --
\r
1132 ./completelinkage.o : completelinkage.cpp
\r
1133 $(CC) $(CC_OPTIONS) completelinkage.cpp -c $(INCLUDE) -o ./completelinkage.o
\r
1136 # Item # 91 -- database --
\r
1137 ./database.o : database.cpp
\r
1138 $(CC) $(CC_OPTIONS) database.cpp -c $(INCLUDE) -o ./database.o
\r
1141 # Item # 92 -- engine --
\r
1142 ./engine.o : engine.cpp
\r
1143 $(CC) $(CC_OPTIONS) engine.cpp -c $(INCLUDE) -o ./engine.o
\r
1146 # Item # 93 -- fastamap --
\r
1147 ./fastamap.o : fastamap.cpp
\r
1148 $(CC) $(CC_OPTIONS) fastamap.cpp -c $(INCLUDE) -o ./fastamap.o
\r
1151 # Item # 94 -- fileoutput --
\r
1152 ./fileoutput.o : fileoutput.cpp
\r
1153 $(CC) $(CC_OPTIONS) fileoutput.cpp -c $(INCLUDE) -o ./fileoutput.o
\r
1156 # Item # 95 -- globaldata --
\r
1157 ./globaldata.o : globaldata.cpp
\r
1158 $(CC) $(CC_OPTIONS) globaldata.cpp -c $(INCLUDE) -o ./globaldata.o
\r
1161 # Item # 96 -- groupmap --
\r
1162 ./groupmap.o : groupmap.cpp
\r
1163 $(CC) $(CC_OPTIONS) groupmap.cpp -c $(INCLUDE) -o ./groupmap.o
\r
1166 # Item # 97 -- helpcommand --
\r
1167 ./helpcommand.o : helpcommand.cpp
\r
1168 $(CC) $(CC_OPTIONS) helpcommand.cpp -c $(INCLUDE) -o ./helpcommand.o
\r
1171 # Item # 98 -- inputdata --
\r
1172 ./inputdata.o : inputdata.cpp
\r
1173 $(CC) $(CC_OPTIONS) inputdata.cpp -c $(INCLUDE) -o ./inputdata.o
\r
1176 # Item # 99 -- jackknife --
\r
1177 ./jackknife.o : jackknife.cpp
\r
1178 $(CC) $(CC_OPTIONS) jackknife.cpp -c $(INCLUDE) -o ./jackknife.o
\r
1181 # Item # 100 -- kmer --
\r
1182 ./kmer.o : kmer.cpp
\r
1183 $(CC) $(CC_OPTIONS) kmer.cpp -c $(INCLUDE) -o ./kmer.o
\r
1186 # Item # 101 -- kmerdb --
\r
1187 ./kmerdb.o : kmerdb.cpp
\r
1188 $(CC) $(CC_OPTIONS) kmerdb.cpp -c $(INCLUDE) -o ./kmerdb.o
\r
1191 # Item # 102 -- listvector --
\r
1192 ./listvector.o : listvector.cpp
\r
1193 $(CC) $(CC_OPTIONS) listvector.cpp -c $(INCLUDE) -o ./listvector.o
\r
1196 # Item # 103 -- mothur --
\r
1197 ./mothur.o : mothur.cpp
\r
1198 $(CC) $(CC_OPTIONS) mothur.cpp -c $(INCLUDE) -o ./mothur.o
\r
1201 # Item # 104 -- nameassignment --
\r
1202 ./nameassignment.o : nameassignment.cpp
\r
1203 $(CC) $(CC_OPTIONS) nameassignment.cpp -c $(INCLUDE) -o ./nameassignment.o
\r
1206 # Item # 105 -- npshannon --
\r
1207 ./npshannon.o : npshannon.cpp
\r
1208 $(CC) $(CC_OPTIONS) npshannon.cpp -c $(INCLUDE) -o ./npshannon.o
\r
1211 # Item # 106 -- ordervector --
\r
1212 ./ordervector.o : ordervector.cpp
\r
1213 $(CC) $(CC_OPTIONS) ordervector.cpp -c $(INCLUDE) -o ./ordervector.o
\r
1216 # Item # 107 -- progress --
\r
1217 ./progress.o : progress.cpp
\r
1218 $(CC) $(CC_OPTIONS) progress.cpp -c $(INCLUDE) -o ./progress.o
\r
1221 # Item # 108 -- quitcommand --
\r
1222 ./quitcommand.o : quitcommand.cpp
\r
1223 $(CC) $(CC_OPTIONS) quitcommand.cpp -c $(INCLUDE) -o ./quitcommand.o
\r
1226 # Item # 109 -- rabundvector --
\r
1227 ./rabundvector.o : rabundvector.cpp
\r
1228 $(CC) $(CC_OPTIONS) rabundvector.cpp -c $(INCLUDE) -o ./rabundvector.o
\r
1231 # Item # 110 -- rarecalc --
\r
1232 ./rarecalc.o : rarecalc.cpp
\r
1233 $(CC) $(CC_OPTIONS) rarecalc.cpp -c $(INCLUDE) -o ./rarecalc.o
\r
1236 # Item # 111 -- raredisplay --
\r
1237 ./raredisplay.o : raredisplay.cpp
\r
1238 $(CC) $(CC_OPTIONS) raredisplay.cpp -c $(INCLUDE) -o ./raredisplay.o
\r
1241 # Item # 112 -- rarefact --
\r
1242 ./rarefact.o : rarefact.cpp
\r
1243 $(CC) $(CC_OPTIONS) rarefact.cpp -c $(INCLUDE) -o ./rarefact.o
\r
1246 # Item # 113 -- rarefactcommand --
\r
1247 ./rarefactcommand.o : rarefactcommand.cpp
\r
1248 $(CC) $(CC_OPTIONS) rarefactcommand.cpp -c $(INCLUDE) -o ./rarefactcommand.o
\r
1251 # Item # 114 -- rarefactsharedcommand --
\r
1252 ./rarefactsharedcommand.o : rarefactsharedcommand.cpp
\r
1253 $(CC) $(CC_OPTIONS) rarefactsharedcommand.cpp -c $(INCLUDE) -o ./rarefactsharedcommand.o
\r
1256 # Item # 115 -- sabundvector --
\r
1257 ./sabundvector.o : sabundvector.cpp
\r
1258 $(CC) $(CC_OPTIONS) sabundvector.cpp -c $(INCLUDE) -o ./sabundvector.o
\r
1261 # Item # 116 -- sequence --
\r
1262 ./sequence.o : sequence.cpp
\r
1263 $(CC) $(CC_OPTIONS) sequence.cpp -c $(INCLUDE) -o ./sequence.o
\r
1266 # Item # 117 -- shannon --
\r
1267 ./shannon.o : shannon.cpp
\r
1268 $(CC) $(CC_OPTIONS) shannon.cpp -c $(INCLUDE) -o ./shannon.o
\r
1271 # Item # 118 -- sharedace --
\r
1272 ./sharedace.o : sharedace.cpp
\r
1273 $(CC) $(CC_OPTIONS) sharedace.cpp -c $(INCLUDE) -o ./sharedace.o
\r
1276 # Item # 119 -- sharedchao1 --
\r
1277 ./sharedchao1.o : sharedchao1.cpp
\r
1278 $(CC) $(CC_OPTIONS) sharedchao1.cpp -c $(INCLUDE) -o ./sharedchao1.o
\r
1281 # Item # 120 -- sharedcommand --
\r
1282 ./sharedcommand.o : sharedcommand.cpp
\r
1283 $(CC) $(CC_OPTIONS) sharedcommand.cpp -c $(INCLUDE) -o ./sharedcommand.o
\r
1286 # Item # 121 -- sharedjabund --
\r
1287 ./sharedjabund.o : sharedjabund.cpp
\r
1288 $(CC) $(CC_OPTIONS) sharedjabund.cpp -c $(INCLUDE) -o ./sharedjabund.o
\r
1291 # Item # 122 -- sharedjclass --
\r
1292 ./sharedjclass.o : sharedjclass.cpp
\r
1293 $(CC) $(CC_OPTIONS) sharedjclass.cpp -c $(INCLUDE) -o ./sharedjclass.o
\r
1296 # Item # 123 -- sharedjest --
\r
1297 ./sharedjest.o : sharedjest.cpp
\r
1298 $(CC) $(CC_OPTIONS) sharedjest.cpp -c $(INCLUDE) -o ./sharedjest.o
\r
1301 # Item # 124 -- sharedordervector --
\r
1302 ./sharedordervector.o : sharedordervector.cpp
\r
1303 $(CC) $(CC_OPTIONS) sharedordervector.cpp -c $(INCLUDE) -o ./sharedordervector.o
\r
1306 # Item # 125 -- sharedrabundvector --
\r
1307 ./sharedrabundvector.o : sharedrabundvector.cpp
\r
1308 $(CC) $(CC_OPTIONS) sharedrabundvector.cpp -c $(INCLUDE) -o ./sharedrabundvector.o
\r
1311 # Item # 126 -- sharedsabundvector --
\r
1312 ./sharedsabundvector.o : sharedsabundvector.cpp
\r
1313 $(CC) $(CC_OPTIONS) sharedsabundvector.cpp -c $(INCLUDE) -o ./sharedsabundvector.o
\r
1316 # Item # 127 -- sharedsobs --
\r
1317 ./sharedsobs.o : sharedsobs.cpp
\r
1318 $(CC) $(CC_OPTIONS) sharedsobs.cpp -c $(INCLUDE) -o ./sharedsobs.o
\r
1321 # Item # 128 -- sharedsorabund --
\r
1322 ./sharedsorabund.o : sharedsorabund.cpp
\r
1323 $(CC) $(CC_OPTIONS) sharedsorabund.cpp -c $(INCLUDE) -o ./sharedsorabund.o
\r
1326 # Item # 129 -- sharedsorclass --
\r
1327 ./sharedsorclass.o : sharedsorclass.cpp
\r
1328 $(CC) $(CC_OPTIONS) sharedsorclass.cpp -c $(INCLUDE) -o ./sharedsorclass.o
\r
1331 # Item # 130 -- sharedsorest --
\r
1332 ./sharedsorest.o : sharedsorest.cpp
\r
1333 $(CC) $(CC_OPTIONS) sharedsorest.cpp -c $(INCLUDE) -o ./sharedsorest.o
\r
1336 # Item # 131 -- sharedthetan --
\r
1337 ./sharedthetan.o : sharedthetan.cpp
\r
1338 $(CC) $(CC_OPTIONS) sharedthetan.cpp -c $(INCLUDE) -o ./sharedthetan.o
\r
1341 # Item # 132 -- sharedthetayc --
\r
1342 ./sharedthetayc.o : sharedthetayc.cpp
\r
1343 $(CC) $(CC_OPTIONS) sharedthetayc.cpp -c $(INCLUDE) -o ./sharedthetayc.o
\r
1346 # Item # 133 -- simpson --
\r
1347 ./simpson.o : simpson.cpp
\r
1348 $(CC) $(CC_OPTIONS) simpson.cpp -c $(INCLUDE) -o ./simpson.o
\r
1351 # Item # 134 -- singlelinkage --
\r
1352 ./singlelinkage.o : singlelinkage.cpp
\r
1353 $(CC) $(CC_OPTIONS) singlelinkage.cpp -c $(INCLUDE) -o ./singlelinkage.o
\r
1356 # Item # 135 -- sparsematrix --
\r
1357 ./sparsematrix.o : sparsematrix.cpp
\r
1358 $(CC) $(CC_OPTIONS) sparsematrix.cpp -c $(INCLUDE) -o ./sparsematrix.o
\r
1361 # Item # 136 -- summarycommand --
\r
1362 ./summarycommand.o : summarycommand.cpp
\r
1363 $(CC) $(CC_OPTIONS) summarycommand.cpp -c $(INCLUDE) -o ./summarycommand.o
\r
1366 # Item # 137 -- summarysharedcommand --
\r
1367 ./summarysharedcommand.o : summarysharedcommand.cpp
\r
1368 $(CC) $(CC_OPTIONS) summarysharedcommand.cpp -c $(INCLUDE) -o ./summarysharedcommand.o
\r
1371 # Item # 138 -- uvest --
\r
1372 ./uvest.o : uvest.cpp
\r
1373 $(CC) $(CC_OPTIONS) uvest.cpp -c $(INCLUDE) -o ./uvest.o
\r
1376 # Item # 139 -- validcalculator --
\r
1377 ./validcalculator.o : validcalculator.cpp
\r
1378 $(CC) $(CC_OPTIONS) validcalculator.cpp -c $(INCLUDE) -o ./validcalculator.o
\r
1381 # Item # 140 -- validparameter --
\r
1382 ./validparameter.o : validparameter.cpp
\r
1383 $(CC) $(CC_OPTIONS) validparameter.cpp -c $(INCLUDE) -o ./validparameter.o
\r
1386 # Item # 141 -- treenode --
\r
1387 ./treenode.o : treenode.cpp
\r
1388 $(CC) $(CC_OPTIONS) treenode.cpp -c $(INCLUDE) -o ./treenode.o
\r
1391 # Item # 142 -- readtreecommand --
\r
1392 ./readtreecommand.o : readtreecommand.cpp
\r
1393 $(CC) $(CC_OPTIONS) readtreecommand.cpp -c $(INCLUDE) -o ./readtreecommand.o
\r
1396 # Item # 143 -- reversecommand --
\r
1397 ./reversecommand.o : reversecommand.cpp
\r
1398 $(CC) $(CC_OPTIONS) reversecommand.cpp -c $(INCLUDE) -o ./reversecommand.o
\r
1401 # Item # 144 -- trimseqscommand --
\r
1402 ./trimseqscommand.o : trimseqscommand.cpp
\r
1403 $(CC) $(CC_OPTIONS) trimseqscommand.cpp -c $(INCLUDE) -o ./trimseqscommand.o
\r
1406 # Item # 145 -- slibshuff --
\r
1407 ./slibshuff.o : slibshuff.cpp
\r
1408 $(CC) $(CC_OPTIONS) slibshuff.cpp -c $(INCLUDE) -o ./slibshuff.o
\r
1411 # Item # 146 -- libshuff --
\r
1412 ./libshuff.o : libshuff.cpp
\r
1413 $(CC) $(CC_OPTIONS) libshuff.cpp -c $(INCLUDE) -o ./libshuff.o
\r
1416 # Item # 147 -- dlibshuff --
\r
1417 ./dlibshuff.o : dlibshuff.cpp
\r
1418 $(CC) $(CC_OPTIONS) dlibshuff.cpp -c $(INCLUDE) -o ./dlibshuff.o
\r
1421 # Item # 148 -- mergefilecommand --
\r
1422 ./mergefilecommand.o : mergefilecommand.cpp
\r
1423 $(CC) $(CC_OPTIONS) mergefilecommand.cpp -c $(INCLUDE) -o ./mergefilecommand.o
\r
1426 # Item # 149 -- coverage --
\r
1427 ./coverage.o : coverage.cpp
\r
1428 $(CC) $(CC_OPTIONS) coverage.cpp -c $(INCLUDE) -o ./coverage.o
\r
1431 # Item # 150 -- whittaker --
\r
1432 ./whittaker.o : whittaker.cpp
\r
1433 $(CC) $(CC_OPTIONS) whittaker.cpp -c $(INCLUDE) -o ./whittaker.o
\r
1436 # Item # 151 -- preclustercommand --
\r
1437 ./preclustercommand.o : preclustercommand.cpp
\r
1438 $(CC) $(CC_OPTIONS) preclustercommand.cpp -c $(INCLUDE) -o ./preclustercommand.o
\r
1441 # Item # 152 -- otuhierarchycommand --
\r
1442 ./otuhierarchycommand.o : otuhierarchycommand.cpp
\r
1443 $(CC) $(CC_OPTIONS) otuhierarchycommand.cpp -c $(INCLUDE) -o ./otuhierarchycommand.o
\r
1446 # Item # 153 -- setdircommand --
\r
1447 ./setdircommand.o : setdircommand.cpp
\r
1448 $(CC) $(CC_OPTIONS) setdircommand.cpp -c $(INCLUDE) -o ./setdircommand.o
\r
1451 # Item # 154 -- getgroupcommand --
\r
1452 ./getgroupcommand.o : getgroupcommand.cpp
\r
1453 $(CC) $(CC_OPTIONS) getgroupcommand.cpp -c $(INCLUDE) -o ./getgroupcommand.o
\r
1456 # Item # 155 -- getlabelcommand --
\r
1457 ./getlabelcommand.o : getlabelcommand.cpp
\r
1458 $(CC) $(CC_OPTIONS) getlabelcommand.cpp -c $(INCLUDE) -o ./getlabelcommand.o
\r
1461 # Item # 156 -- secondarystructurecommand --
\r
1462 ./secondarystructurecommand.o : secondarystructurecommand.cpp
\r
1463 $(CC) $(CC_OPTIONS) secondarystructurecommand.cpp -c $(INCLUDE) -o ./secondarystructurecommand.o
\r
1466 # Item # 157 -- mothurout --
\r
1467 ./mothurout.o : mothurout.cpp
\r
1468 $(CC) $(CC_OPTIONS) mothurout.cpp -c $(INCLUDE) -o ./mothurout.o
\r
1471 # Item # 158 -- parselistscommand --
\r
1472 ./parselistscommand.o : parselistscommand.cpp
\r
1473 $(CC) $(CC_OPTIONS) parselistscommand.cpp -c $(INCLUDE) -o ./parselistscommand.o
\r
1476 # Item # 159 -- readblast --
\r
1477 ./readblast.o : readblast.cpp
\r
1478 $(CC) $(CC_OPTIONS) readblast.cpp -c $(INCLUDE) -o ./readblast.o
\r
1481 # Item # 160 -- chimeracheckrdp --
\r
1482 ./chimeracheckrdp.o : chimeracheckrdp.cpp
\r
1483 $(CC) $(CC_OPTIONS) chimeracheckrdp.cpp -c $(INCLUDE) -o ./chimeracheckrdp.o
\r
1486 # Item # 161 -- hclustercommand --
\r
1487 ./hclustercommand.o : hclustercommand.cpp
\r
1488 $(CC) $(CC_OPTIONS) hclustercommand.cpp -c $(INCLUDE) -o ./hclustercommand.o
\r
1491 # Item # 162 -- hcluster --
\r
1492 ./hcluster.o : hcluster.cpp
\r
1493 $(CC) $(CC_OPTIONS) hcluster.cpp -c $(INCLUDE) -o ./hcluster.o
\r
1496 # Item # 163 -- getlistcountcommand --
\r
1497 ./getlistcountcommand.o : getlistcountcommand.cpp
\r
1498 $(CC) $(CC_OPTIONS) getlistcountcommand.cpp -c $(INCLUDE) -o ./getlistcountcommand.o
\r
1501 # Item # 164 -- readcluster --
\r
1502 ./readcluster.o : readcluster.cpp
\r
1503 $(CC) $(CC_OPTIONS) readcluster.cpp -c $(INCLUDE) -o ./readcluster.o
\r
1506 # Item # 165 -- ccode --
\r
1507 ./ccode.o : ccode.cpp
\r
1508 $(CC) $(CC_OPTIONS) ccode.cpp -c $(INCLUDE) -o ./ccode.o
\r
1511 # Item # 166 -- taxonomyequalizer --
\r
1512 ./taxonomyequalizer.o : taxonomyequalizer.cpp
\r
1513 $(CC) $(CC_OPTIONS) taxonomyequalizer.cpp -c $(INCLUDE) -o ./taxonomyequalizer.o
\r
1516 # Item # 167 -- phylotypecommand --
\r
1517 ./phylotypecommand.o : phylotypecommand.cpp
\r
1518 $(CC) $(CC_OPTIONS) phylotypecommand.cpp -c $(INCLUDE) -o ./phylotypecommand.o
\r
1521 # Item # 168 -- classifyseqscommand --
\r
1522 ./classifyseqscommand.o : classifyseqscommand.cpp
\r
1523 $(CC) $(CC_OPTIONS) classifyseqscommand.cpp -c $(INCLUDE) -o ./classifyseqscommand.o
\r
1526 # Item # 169 -- classify --
\r
1527 ./classify.o : classify.cpp
\r
1528 $(CC) $(CC_OPTIONS) classify.cpp -c $(INCLUDE) -o ./classify.o
\r
1531 # Item # 170 -- phylotree --
\r
1532 ./phylotree.o : phylotree.cpp
\r
1533 $(CC) $(CC_OPTIONS) phylotree.cpp -c $(INCLUDE) -o ./phylotree.o
\r
1536 # Item # 171 -- bayesian --
\r
1537 ./bayesian.o : bayesian.cpp
\r
1538 $(CC) $(CC_OPTIONS) bayesian.cpp -c $(INCLUDE) -o ./bayesian.o
\r
1541 # Item # 172 -- alignmentdb --
\r
1542 ./alignmentdb.o : alignmentdb.cpp
\r
1543 $(CC) $(CC_OPTIONS) alignmentdb.cpp -c $(INCLUDE) -o ./alignmentdb.o
\r
1546 # Item # 173 -- knn --
\r
1548 $(CC) $(CC_OPTIONS) knn.cpp -c $(INCLUDE) -o ./knn.o
\r
1551 # Item # 174 -- distancedb --
\r
1552 ./distancedb.o : distancedb.cpp
\r
1553 $(CC) $(CC_OPTIONS) distancedb.cpp -c $(INCLUDE) -o ./distancedb.o
\r
1556 # Item # 175 -- chimeraslayer --
\r
1557 ./chimeraslayer.o : chimeraslayer.cpp
\r
1558 $(CC) $(CC_OPTIONS) chimeraslayer.cpp -c $(INCLUDE) -o ./chimeraslayer.o
\r
1561 # Item # 176 -- slayer --
\r
1562 ./slayer.o : slayer.cpp
\r
1563 $(CC) $(CC_OPTIONS) slayer.cpp -c $(INCLUDE) -o ./slayer.o
\r
1566 # Item # 177 -- pcacommand --
\r
1567 ./pcacommand.o : pcacommand.cpp
\r
1568 $(CC) $(CC_OPTIONS) pcacommand.cpp -c $(INCLUDE) -o ./pcacommand.o
\r
1571 # Item # 178 -- formatcolumn --
\r
1572 ./formatcolumn.o : formatcolumn.cpp
\r
1573 $(CC) $(CC_OPTIONS) formatcolumn.cpp -c $(INCLUDE) -o ./formatcolumn.o
\r
1576 # Item # 179 -- formatphylip --
\r
1577 ./formatphylip.o : formatphylip.cpp
\r
1578 $(CC) $(CC_OPTIONS) formatphylip.cpp -c $(INCLUDE) -o ./formatphylip.o
\r
1581 # Item # 180 -- mgclustercommand --
\r
1582 ./mgclustercommand.o : mgclustercommand.cpp
\r
1583 $(CC) $(CC_OPTIONS) mgclustercommand.cpp -c $(INCLUDE) -o ./mgclustercommand.o
\r
1586 # Item # 181 -- getsharedotucommand --
\r
1587 ./getsharedotucommand.o : getsharedotucommand.cpp
\r
1588 $(CC) $(CC_OPTIONS) getsharedotucommand.cpp -c $(INCLUDE) -o ./getsharedotucommand.o
\r
1591 # Item # 182 -- maligner --
\r
1592 ./maligner.o : maligner.cpp
\r
1593 $(CC) $(CC_OPTIONS) maligner.cpp -c $(INCLUDE) -o ./maligner.o
\r
1596 # Item # 183 -- chimerarealigner --
\r
1597 ./chimerarealigner.o : chimerarealigner.cpp
\r
1598 $(CC) $(CC_OPTIONS) chimerarealigner.cpp -c $(INCLUDE) -o ./chimerarealigner.o
\r
1601 # Item # 184 -- bergerparker --
\r
1602 ./bergerparker.o : bergerparker.cpp
\r
1603 $(CC) $(CC_OPTIONS) bergerparker.cpp -c $(INCLUDE) -o ./bergerparker.o
\r
1606 # Item # 185 -- bstick --
\r
1607 ./bstick.o : bstick.cpp
\r
1608 $(CC) $(CC_OPTIONS) bstick.cpp -c $(INCLUDE) -o ./bstick.o
\r
1611 # Item # 186 -- sharedkstest --
\r
1612 ./sharedkstest.o : sharedkstest.cpp
\r
1613 $(CC) $(CC_OPTIONS) sharedkstest.cpp -c $(INCLUDE) -o ./sharedkstest.o
\r
1616 # Item # 187 -- qstat --
\r
1617 ./qstat.o : qstat.cpp
\r
1618 $(CC) $(CC_OPTIONS) qstat.cpp -c $(INCLUDE) -o ./qstat.o
\r
1621 # Item # 188 -- shen --
\r
1622 ./shen.o : shen.cpp
\r
1623 $(CC) $(CC_OPTIONS) shen.cpp -c $(INCLUDE) -o ./shen.o
\r
1626 # Item # 189 -- logsd --
\r
1627 ./logsd.o : logsd.cpp
\r
1628 $(CC) $(CC_OPTIONS) logsd.cpp -c $(INCLUDE) -o ./logsd.o
\r
1631 # Item # 190 -- geom --
\r
1632 ./geom.o : geom.cpp
\r
1633 $(CC) $(CC_OPTIONS) geom.cpp -c $(INCLUDE) -o ./geom.o
\r
1635 # Item # 191 -- parsesffcommand --
\r
1636 ./parsesffcommand.o : parsesffcommand.cpp
\r
1637 $(CC) $(CC_OPTIONS) parsesffcommand.cpp -c $(INCLUDE) -o ./parsesffcommand.o
\r
1639 # Item # 192 -- chimeraccodecommand --
\r
1640 ./chimeraccodecommand.o : chimeraccodecommand.cpp
\r
1641 $(CC) $(CC_OPTIONS) chimeraccodecommand.cpp -c $(INCLUDE) -o ./chimeraccodecommand.o
\r
1643 # Item # 193 -- chimeracheckcommand --
\r
1644 ./chimeracheckcommand.o : chimeracheckcommand.cpp
\r
1645 $(CC) $(CC_OPTIONS) chimeracheckcommand.cpp -c $(INCLUDE) -o ./chimeracheckcommand.o
\r
1648 # Item # 194 -- chimeraslayercommand --
\r
1649 ./chimeraslayercommand.o : chimeraslayercommand.cpp
\r
1650 $(CC) $(CC_OPTIONS) chimeraslayercommand.cpp -c $(INCLUDE) -o ./chimeraslayercommand.o
\r
1652 # Item # 195 -- chimerapintailcommand --
\r
1653 ./chimerapintailcommand.o : chimerapintailcommand.cpp
\r
1654 $(CC) $(CC_OPTIONS) chimerapintailcommand.cpp -c $(INCLUDE) -o ./chimerapintailcommand.o
\r
1656 # Item # 196 -- chimerabellerophoncommand --
\r
1657 ./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp
\r
1658 $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o
\r
1660 # Item # 197 -- phylosummary --
\r
1661 ./phylosummary.o : phylosummary.cpp
\r
1662 $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o
\r
1664 # Item # 198 -- setlogfilecommand --
\r
1665 ./setlogfilecommand.o : setlogfilecommand.cpp
\r
1666 $(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o
\r
1668 # Item # 199 -- phylodiversity --
\r
1669 ./phylodiversity.o : phylodiversity.cpp
\r
1670 $(CC) $(CC_OPTIONS) phylodiversity.cpp -c $(INCLUDE) -o ./phylodiversity.o
\r
1672 # Item # 200 -- phylodiversitycommand --
\r
1673 ./phylodiversitycommand.o : phylodiversitycommand.cpp
\r
1674 $(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o
\r
1676 # Item # 201 -- makegroupcommand --
\r
1677 ./makegroupcommand.o : makegroupcommand.cpp
\r
1678 $(CC) $(CC_OPTIONS) makegroupcommand.cpp -c $(INCLUDE) -o ./makegroupcommand.o
\r
1680 # Item # 202 -- chopseqscommand --
\r
1681 ./chopseqscommand.o : chopseqscommand.cpp
\r
1682 $(CC) $(CC_OPTIONS) chopseqscommand.cpp -c $(INCLUDE) -o ./chopseqscommand.o
\r
1684 # Item # 203 -- clearcutcommand --
\r
1685 ./clearcutcommand.o : clearcutcommand.cpp
\r
1686 $(CC) $(CC_OPTIONS) clearcutcommand.cpp -c $(INCLUDE) -o ./clearcutcommand.o
\r
1688 # Item # 204 -- catchallcommand --
\r
1689 ./catchallcommand.o : catchallcommand.cpp
\r
1690 $(CC) $(CC_OPTIONS) catchallcommand.cpp -c $(INCLUDE) -o ./catchallcommand.o
\r
1692 # Item # 205 -- splitabundcommand --
\r
1693 ./splitabundcommand.o : splitabundcommand.cpp
\r
1694 $(CC) $(CC_OPTIONS) splitabundcommand.cpp -c $(INCLUDE) -o ./splitabundcommand.o
\r
1696 # Item # 206 -- splitmatrix --
\r
1697 ./splitmatrix.o : splitmatrix.cpp
\r
1698 $(CC) $(CC_OPTIONS) splitmatrix.cpp -c $(INCLUDE) -o ./splitmatrix.o
\r
1700 # Item # 207 -- splitmatrix --
\r
1701 ./clustersplitcommand.o : clustersplitcommand.cpp
\r
1702 $(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o
\r
1704 # Item # 207 -- splitmatrix --
\r
1705 ./classifyotucommand.o : classifyotucommand.cpp
\r
1706 $(CC) $(CC_OPTIONS) classifyotucommand.cpp -c $(INCLUDE) -o ./classifyotucommand.o
\r
1709 ##### END RUN ####
\r