1 ###################################################
4 # Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41]
5 # Created: April 16, 2010
7 ###################################################
16 # if you do not want to use the readline library set to no, default yes.
17 # make sure you have the library installed
21 ifeq ($(strip $(USEREADLINE)),yes)
22 CC_OPTIONS += -DUSE_READLINE
32 ifeq ($(strip $(USEMPI)),yes)
33 CC_OPTIONS += -DUSE_MPI
37 # INCLUDE directories for mothur
48 ./treegroupscommand.o\
49 ./bootstrapsharedcommand.o\
50 ./matrixoutputcommand.o\
52 ./screenseqscommand.o\
74 ./unifracweightedcommand.o\
77 ./unifracunweightedcommand.o\
93 ./sharedkulczynskicody.o\
94 ./sharedmorisitahorn.o\
100 ./heatmapsimcommand.o\
103 ./filterseqscommand.o\
107 ./sharedmarczewski.o\
110 ./parsimonycommand.o\
112 ./seqsummarycommand.o\
113 ./chimeraccodecommand.o\
114 ./chimerabellerophoncommand.o\
115 ./chimeracheckcommand.o\
116 ./chimeraslayercommand.o\
117 ./chimerapintailcommand.o\
118 ./chimeraseqscommand.o\
119 ./sharedlistvector.o\
122 ./sharedsobscollectsummary.o\
123 ./deconvolutecommand.o\
126 ./removeseqscommand.o\
128 ./binsequencecommand.o\
139 ./collectsharedcommand.o\
140 ./commandoptionparser.o\
149 ./makegroupcommand.o\
153 ./splitabundcommand.o\
170 ./rarefactsharedcommand.o\
180 ./sharedordervector.o\
181 ./sharedrabundvector.o\
182 ./sharedsabundvector.o\
193 ./summarysharedcommand.o\
204 ./mergefilecommand.o\
207 ./preclustercommand.o\
208 ./otuhierarchycommand.o\
212 ./secondarystructurecommand.o\
214 ./parselistscommand.o\
219 ./getlistcountcommand.o\
222 ./taxonomyequalizer.o\
223 ./phylotypecommand.o\
224 ./classifyseqscommand.o\
229 ./phylodiversitycommand.o\
240 ./mgclustercommand.o\
241 ./getsharedotucommand.o\
243 ./chimerarealigner.o\
251 ./setlogfilecommand.o
252 $(CC) $(LNK_OPTIONS) \
254 ./treegroupscommand.o\
255 ./bootstrapsharedcommand.o\
256 ./matrixoutputcommand.o\
257 ./getoturepcommand.o\
258 ./screenseqscommand.o\
268 ./needlemanoverlap.o\
280 ./unifracweightedcommand.o\
283 ./unifracunweightedcommand.o\
284 ./getsabundcommand.o\
285 ./getrabundcommand.o\
288 ./sharedanderbergs.o\
296 ./sharedbraycurtis.o\
297 ./sharedkulczynski.o\
299 ./sharedkulczynskicody.o\
300 ./sharedmorisitahorn.o\
305 ./consensuscommand.o\
306 ./heatmapsimcommand.o\
309 ./filterseqscommand.o\
313 ./sharedmarczewski.o\
316 ./parsimonycommand.o\
318 ./seqsummarycommand.o\
319 ./chimeraccodecommand.o\
320 ./chimerabellerophoncommand.o\
321 ./chimeracheckcommand.o\
322 ./chimeraslayercommand.o\
323 ./chimerapintailcommand.o\
324 ./chimeraseqscommand.o\
325 ./sharedlistvector.o\
328 ./sharedsobscollectsummary.o\
329 ./deconvolutecommand.o\
332 ./removeseqscommand.o\
334 ./binsequencecommand.o\
345 ./collectsharedcommand.o\
346 ./commandoptionparser.o\
355 ./makegroupcommand.o\
359 ./splitabundcommand.o\
376 ./rarefactsharedcommand.o\
386 ./sharedordervector.o\
387 ./sharedrabundvector.o\
388 ./sharedsabundvector.o\
399 ./summarysharedcommand.o\
410 ./mergefilecommand.o\
413 ./preclustercommand.o\
414 ./otuhierarchycommand.o\
418 ./secondarystructurecommand.o\
420 ./parselistscommand.o\
425 ./getlistcountcommand.o\
428 ./taxonomyequalizer.o\
429 ./phylotypecommand.o\
430 ./classifyseqscommand.o\
435 ./phylodiversitycommand.o\
446 ./mgclustercommand.o\
447 ./getsharedotucommand.o\
449 ./chimerarealigner.o\
457 ./setlogfilecommand.o\
463 ./treegroupscommand.o\
464 ./bootstrapsharedcommand.o\
465 ./matrixoutputcommand.o\
466 ./getoturepcommand.o\
467 ./screenseqscommand.o\
477 ./needlemanoverlap.o\
489 ./unifracweightedcommand.o\
492 ./unifracunweightedcommand.o\
493 ./getsabundcommand.o\
494 ./getrabundcommand.o\
497 ./sharedanderbergs.o\
505 ./sharedbraycurtis.o\
506 ./sharedkulczynski.o\
508 ./sharedkulczynskicody.o\
509 ./sharedmorisitahorn.o\
514 ./consensuscommand.o\
515 ./heatmapsimcommand.o\
518 ./filterseqscommand.o\
522 ./sharedmarczewski.o\
525 ./parsimonycommand.o\
527 ./seqsummarycommand.o\
528 ./chimeraccodecommand.o\
529 ./chimerabellerophoncommand.o\
530 ./chimeracheckcommand.o\
531 ./chimeraslayercommand.o\
532 ./chimerapintailcommand.o\
533 ./chimeraseqscommand.o\
534 ./sharedlistvector.o\
537 ./sharedsobscollectsummary.o\
538 ./deconvolutecommand.o\
541 ./removeseqscommand.o\
543 ./binsequencecommand.o\
554 ./collectsharedcommand.o\
555 ./commandoptionparser.o\
564 ./makegroupcommand.o\
568 ./splitabundcommand.o\
585 ./rarefactsharedcommand.o\
595 ./sharedordervector.o\
596 ./sharedrabundvector.o\
597 ./sharedsabundvector.o\
608 ./summarysharedcommand.o\
619 ./mergefilecommand.o\
622 ./preclustercommand.o\
623 ./otuhierarchycommand.o\
627 ./secondarystructurecommand.o\
629 ./parselistscommand.o\
634 ./getlistcountcommand.o\
637 ./taxonomyequalizer.o\
638 ./phylotypecommand.o\
639 ./classifyseqscommand.o\
644 ./phylodiversitycommand.o\
655 ./mgclustercommand.o\
656 ./getsharedotucommand.o\
658 ./chimerarealigner.o\
666 ./setlogfilecommand.o\
670 #cp mothur ../Release/mothur
673 # Build the parts of mothur
677 # Item # 1 -- sharedutilities --
678 ./sharedutilities.o : sharedutilities.cpp
679 $(CC) $(CC_OPTIONS) sharedutilities.cpp -c $(INCLUDE) -o ./sharedutilities.o
682 # Item # 2 -- treegroupscommand --
683 ./treegroupscommand.o : treegroupscommand.cpp
684 $(CC) $(CC_OPTIONS) treegroupscommand.cpp -c $(INCLUDE) -o ./treegroupscommand.o
687 # Item # 3 -- bootstrapsharedcommand --
688 ./bootstrapsharedcommand.o : bootstrapsharedcommand.cpp
689 $(CC) $(CC_OPTIONS) bootstrapsharedcommand.cpp -c $(INCLUDE) -o ./bootstrapsharedcommand.o
692 # Item # 4 -- matrixoutputcommand --
693 ./matrixoutputcommand.o : matrixoutputcommand.cpp
694 $(CC) $(CC_OPTIONS) matrixoutputcommand.cpp -c $(INCLUDE) -o ./matrixoutputcommand.o
697 # Item # 5 -- getoturepcommand --
698 ./getoturepcommand.o : getoturepcommand.cpp
699 $(CC) $(CC_OPTIONS) getoturepcommand.cpp -c $(INCLUDE) -o ./getoturepcommand.o
702 # Item # 6 -- screenseqscommand --
703 ./screenseqscommand.o : screenseqscommand.cpp
704 $(CC) $(CC_OPTIONS) screenseqscommand.cpp -c $(INCLUDE) -o ./screenseqscommand.o
707 # Item # 7 -- chimera --
708 ./chimera.o : chimera.cpp
709 $(CC) $(CC_OPTIONS) chimera.cpp -c $(INCLUDE) -o ./chimera.o
712 # Item # 8 -- decalc --
713 ./decalc.o : decalc.cpp
714 $(CC) $(CC_OPTIONS) decalc.cpp -c $(INCLUDE) -o ./decalc.o
717 # Item # 9 -- readotucommand --
718 ./readotucommand.o : readotucommand.cpp
719 $(CC) $(CC_OPTIONS) readotucommand.cpp -c $(INCLUDE) -o ./readotucommand.o
722 # Item # 10 -- readdistcommand --
723 ./readdistcommand.o : readdistcommand.cpp
724 $(CC) $(CC_OPTIONS) readdistcommand.cpp -c $(INCLUDE) -o ./readdistcommand.o
727 # Item # 11 -- commandfactory --
728 ./commandfactory.o : commandfactory.cpp
729 $(CC) $(CC_OPTIONS) commandfactory.cpp -c $(INCLUDE) -o ./commandfactory.o
732 # Item # 12 -- alignment --
733 ./alignment.o : alignment.cpp
734 $(CC) $(CC_OPTIONS) alignment.cpp -c $(INCLUDE) -o ./alignment.o
737 # Item # 13 -- alignmentcell --
738 ./alignmentcell.o : alignmentcell.cpp
739 $(CC) $(CC_OPTIONS) alignmentcell.cpp -c $(INCLUDE) -o ./alignmentcell.o
742 # Item # 14 -- gotohoverlap --
743 ./gotohoverlap.o : gotohoverlap.cpp
744 $(CC) $(CC_OPTIONS) gotohoverlap.cpp -c $(INCLUDE) -o ./gotohoverlap.o
747 # Item # 15 -- overlap --
748 ./overlap.o : overlap.cpp
749 $(CC) $(CC_OPTIONS) overlap.cpp -c $(INCLUDE) -o ./overlap.o
752 # Item # 16 -- needlemanoverlap --
753 ./needlemanoverlap.o : needlemanoverlap.cpp
754 $(CC) $(CC_OPTIONS) needlemanoverlap.cpp -c $(INCLUDE) -o ./needlemanoverlap.o
757 # Item # 17 -- blastalign --
758 ./blastalign.o : blastalign.cpp
759 $(CC) $(CC_OPTIONS) blastalign.cpp -c $(INCLUDE) -o ./blastalign.o
762 # Item # 18 -- noalign --
763 ./noalign.o : noalign.cpp
764 $(CC) $(CC_OPTIONS) noalign.cpp -c $(INCLUDE) -o ./noalign.o
767 # Item # 19 -- suffixdb --
768 ./suffixdb.o : suffixdb.cpp
769 $(CC) $(CC_OPTIONS) suffixdb.cpp -c $(INCLUDE) -o ./suffixdb.o
772 # Item # 20 -- suffixnodes --
773 ./suffixnodes.o : suffixnodes.cpp
774 $(CC) $(CC_OPTIONS) suffixnodes.cpp -c $(INCLUDE) -o ./suffixnodes.o
777 # Item # 21 -- suffixtree --
778 ./suffixtree.o : suffixtree.cpp
779 $(CC) $(CC_OPTIONS) suffixtree.cpp -c $(INCLUDE) -o ./suffixtree.o
782 # Item # 22 -- blastdb --
783 ./blastdb.o : blastdb.cpp
784 $(CC) $(CC_OPTIONS) blastdb.cpp -c $(INCLUDE) -o ./blastdb.o
787 # Item # 23 -- nast --
789 $(CC) $(CC_OPTIONS) nast.cpp -c $(INCLUDE) -o ./nast.o
792 # Item # 24 -- nastreport --
793 ./nastreport.o : nastreport.cpp
794 $(CC) $(CC_OPTIONS) nastreport.cpp -c $(INCLUDE) -o ./nastreport.o
797 # Item # 25 -- boneh --
798 ./boneh.o : boneh.cpp
799 $(CC) $(CC_OPTIONS) boneh.cpp -c $(INCLUDE) -o ./boneh.o
802 # Item # 26 -- efron --
803 ./efron.o : efron.cpp
804 $(CC) $(CC_OPTIONS) efron.cpp -c $(INCLUDE) -o ./efron.o
807 # Item # 27 -- solow --
808 ./solow.o : solow.cpp
809 $(CC) $(CC_OPTIONS) solow.cpp -c $(INCLUDE) -o ./solow.o
812 # Item # 28 -- unifracweightedcommand --
813 ./unifracweightedcommand.o : unifracweightedcommand.cpp
814 $(CC) $(CC_OPTIONS) unifracweightedcommand.cpp -c $(INCLUDE) -o ./unifracweightedcommand.o
817 # Item # 29 -- weighted --
818 ./weighted.o : weighted.cpp
819 $(CC) $(CC_OPTIONS) weighted.cpp -c $(INCLUDE) -o ./weighted.o
822 # Item # 30 -- unweighted --
823 ./unweighted.o : unweighted.cpp
824 $(CC) $(CC_OPTIONS) unweighted.cpp -c $(INCLUDE) -o ./unweighted.o
827 # Item # 31 -- unifracunweightedcommand --
828 ./unifracunweightedcommand.o : unifracunweightedcommand.cpp
829 $(CC) $(CC_OPTIONS) unifracunweightedcommand.cpp -c $(INCLUDE) -o ./unifracunweightedcommand.o
832 # Item # 32 -- getsabundcommand --
833 ./getsabundcommand.o : getsabundcommand.cpp
834 $(CC) $(CC_OPTIONS) getsabundcommand.cpp -c $(INCLUDE) -o ./getsabundcommand.o
837 # Item # 33 -- getrabundcommand --
838 ./getrabundcommand.o : getrabundcommand.cpp
839 $(CC) $(CC_OPTIONS) getrabundcommand.cpp -c $(INCLUDE) -o ./getrabundcommand.o
842 # Item # 34 -- bellerophon --
843 ./bellerophon.o : bellerophon.cpp
844 $(CC) $(CC_OPTIONS) bellerophon.cpp -c $(INCLUDE) -o ./bellerophon.o
847 # Item # 35 -- pintail --
848 ./pintail.o : pintail.cpp
849 $(CC) $(CC_OPTIONS) pintail.cpp -c $(INCLUDE) -o ./pintail.o
852 # Item # 36 -- sharedanderbergs --
853 ./sharedanderbergs.o : sharedanderbergs.cpp
854 $(CC) $(CC_OPTIONS) sharedanderbergs.cpp -c $(INCLUDE) -o ./sharedanderbergs.o
857 # Item # 37 -- venncommand --
858 ./venncommand.o : venncommand.cpp
859 $(CC) $(CC_OPTIONS) venncommand.cpp -c $(INCLUDE) -o ./venncommand.o
862 # Item # 38 -- venn --
864 $(CC) $(CC_OPTIONS) venn.cpp -c $(INCLUDE) -o ./venn.o
867 # Item # 39 -- fullmatrix --
868 ./fullmatrix.o : fullmatrix.cpp
869 $(CC) $(CC_OPTIONS) fullmatrix.cpp -c $(INCLUDE) -o ./fullmatrix.o
872 # Item # 40 -- heatmap --
873 ./heatmap.o : heatmap.cpp
874 $(CC) $(CC_OPTIONS) heatmap.cpp -c $(INCLUDE) -o ./heatmap.o
877 # Item # 41 -- heatmapcommand --
878 ./heatmapcommand.o : heatmapcommand.cpp
879 $(CC) $(CC_OPTIONS) heatmapcommand.cpp -c $(INCLUDE) -o ./heatmapcommand.o
882 # Item # 42 -- libshuffcommand --
883 ./libshuffcommand.o : libshuffcommand.cpp
884 $(CC) $(CC_OPTIONS) libshuffcommand.cpp -c $(INCLUDE) -o ./libshuffcommand.o
887 # Item # 43 -- nocommands --
888 ./nocommands.o : nocommands.cpp
889 $(CC) $(CC_OPTIONS) nocommands.cpp -c $(INCLUDE) -o ./nocommands.o
892 # Item # 44 -- sharedbraycurtis --
893 ./sharedbraycurtis.o : sharedbraycurtis.cpp
894 $(CC) $(CC_OPTIONS) sharedbraycurtis.cpp -c $(INCLUDE) -o ./sharedbraycurtis.o
897 # Item # 45 -- sharedkulczynski --
898 ./sharedkulczynski.o : sharedkulczynski.cpp
899 $(CC) $(CC_OPTIONS) sharedkulczynski.cpp -c $(INCLUDE) -o ./sharedkulczynski.o
902 # Item # 46 -- sharedlennon --
903 ./sharedlennon.o : sharedlennon.cpp
904 $(CC) $(CC_OPTIONS) sharedlennon.cpp -c $(INCLUDE) -o ./sharedlennon.o
907 # Item # 47 -- sharedkulczynskicody --
908 ./sharedkulczynskicody.o : sharedkulczynskicody.cpp
909 $(CC) $(CC_OPTIONS) sharedkulczynskicody.cpp -c $(INCLUDE) -o ./sharedkulczynskicody.o
912 # Item # 48 -- sharedmorisitahorn --
913 ./sharedmorisitahorn.o : sharedmorisitahorn.cpp
914 $(CC) $(CC_OPTIONS) sharedmorisitahorn.cpp -c $(INCLUDE) -o ./sharedmorisitahorn.o
917 # Item # 49 -- sharedochiai --
918 ./sharedochiai.o : sharedochiai.cpp
919 $(CC) $(CC_OPTIONS) sharedochiai.cpp -c $(INCLUDE) -o ./sharedochiai.o
922 # Item # 50 -- readcolumn --
923 ./readcolumn.o : readcolumn.cpp
924 $(CC) $(CC_OPTIONS) readcolumn.cpp -c $(INCLUDE) -o ./readcolumn.o
927 # Item # 51 -- readotu --
928 ./readotu.o : readotu.cpp
929 $(CC) $(CC_OPTIONS) readotu.cpp -c $(INCLUDE) -o ./readotu.o
932 # Item # 52 -- readphylip --
933 ./readphylip.o : readphylip.cpp
934 $(CC) $(CC_OPTIONS) readphylip.cpp -c $(INCLUDE) -o ./readphylip.o
937 # Item # 53 -- consensuscommand --
938 ./consensuscommand.o : consensuscommand.cpp
939 $(CC) $(CC_OPTIONS) consensuscommand.cpp -c $(INCLUDE) -o ./consensuscommand.o
942 # Item # 54 -- heatmapsimcommand --
943 ./heatmapsimcommand.o : heatmapsimcommand.cpp
944 $(CC) $(CC_OPTIONS) heatmapsimcommand.cpp -c $(INCLUDE) -o ./heatmapsimcommand.o
947 # Item # 55 -- heatmapsim --
948 ./heatmapsim.o : heatmapsim.cpp
949 $(CC) $(CC_OPTIONS) heatmapsim.cpp -c $(INCLUDE) -o ./heatmapsim.o
952 # Item # 56 -- optionparser --
953 ./optionparser.o : optionparser.cpp
954 $(CC) $(CC_OPTIONS) optionparser.cpp -c $(INCLUDE) -o ./optionparser.o
957 # Item # 57 -- filterseqscommand --
958 ./filterseqscommand.o : filterseqscommand.cpp
959 $(CC) $(CC_OPTIONS) filterseqscommand.cpp -c $(INCLUDE) -o ./filterseqscommand.o
962 # Item # 58 -- goodscoverage --
963 ./goodscoverage.o : goodscoverage.cpp
964 $(CC) $(CC_OPTIONS) goodscoverage.cpp -c $(INCLUDE) -o ./goodscoverage.o
967 # Item # 59 -- sequencedb --
968 ./sequencedb.o : sequencedb.cpp
969 $(CC) $(CC_OPTIONS) sequencedb.cpp -c $(INCLUDE) -o ./sequencedb.o
972 # Item # 60 -- sharedjackknife --
973 ./sharedjackknife.o : sharedjackknife.cpp
974 $(CC) $(CC_OPTIONS) sharedjackknife.cpp -c $(INCLUDE) -o ./sharedjackknife.o
977 # Item # 61 -- sharedmarczewski --
978 ./sharedmarczewski.o : sharedmarczewski.cpp
979 $(CC) $(CC_OPTIONS) sharedmarczewski.cpp -c $(INCLUDE) -o ./sharedmarczewski.o
982 # Item # 62 -- aligncommand --
983 ./aligncommand.o : aligncommand.cpp
984 $(CC) $(CC_OPTIONS) aligncommand.cpp -c $(INCLUDE) -o ./aligncommand.o
987 # Item # 63 -- treemap --
988 ./treemap.o : treemap.cpp
989 $(CC) $(CC_OPTIONS) treemap.cpp -c $(INCLUDE) -o ./treemap.o
992 # Item # 64 -- parsimonycommand --
993 ./parsimonycommand.o : parsimonycommand.cpp
994 $(CC) $(CC_OPTIONS) parsimonycommand.cpp -c $(INCLUDE) -o ./parsimonycommand.o
997 # Item # 65 -- parsimony --
998 ./parsimony.o : parsimony.cpp
999 $(CC) $(CC_OPTIONS) parsimony.cpp -c $(INCLUDE) -o ./parsimony.o
1002 # Item # 66 -- seqsummarycommand --
1003 ./seqsummarycommand.o : seqsummarycommand.cpp
1004 $(CC) $(CC_OPTIONS) seqsummarycommand.cpp -c $(INCLUDE) -o ./seqsummarycommand.o
1007 # Item # 67 -- chimeraseqscommand --
1008 ./chimeraseqscommand.o : chimeraseqscommand.cpp
1009 $(CC) $(CC_OPTIONS) chimeraseqscommand.cpp -c $(INCLUDE) -o ./chimeraseqscommand.o
1012 # Item # 68 -- sharedlistvector --
1013 ./sharedlistvector.o : sharedlistvector.cpp
1014 $(CC) $(CC_OPTIONS) sharedlistvector.cpp -c $(INCLUDE) -o ./sharedlistvector.o
1017 # Item # 69 -- tree --
1019 $(CC) $(CC_OPTIONS) tree.cpp -c $(INCLUDE) -o ./tree.o
1022 # Item # 70 -- readtree --
1023 ./readtree.o : readtree.cpp
1024 $(CC) $(CC_OPTIONS) readtree.cpp -c $(INCLUDE) -o ./readtree.o
1027 # Item # 71 -- sharedsobscollectsummary --
1028 ./sharedsobscollectsummary.o : sharedsobscollectsummary.cpp
1029 $(CC) $(CC_OPTIONS) sharedsobscollectsummary.cpp -c $(INCLUDE) -o ./sharedsobscollectsummary.o
1032 # Item # 72 -- deconvolutecommand --
1033 ./deconvolutecommand.o : deconvolutecommand.cpp
1034 $(CC) $(CC_OPTIONS) deconvolutecommand.cpp -c $(INCLUDE) -o ./deconvolutecommand.o
1037 # Item # 73 -- listseqscommand --
1038 ./listseqscommand.o : listseqscommand.cpp
1039 $(CC) $(CC_OPTIONS) listseqscommand.cpp -c $(INCLUDE) -o ./listseqscommand.o
1042 # Item # 74 -- getseqscommand --
1043 ./getseqscommand.o : getseqscommand.cpp
1044 $(CC) $(CC_OPTIONS) getseqscommand.cpp -c $(INCLUDE) -o ./getseqscommand.o
1047 # Item # 75 -- removeseqscommand --
1048 ./removeseqscommand.o : removeseqscommand.cpp
1049 $(CC) $(CC_OPTIONS) removeseqscommand.cpp -c $(INCLUDE) -o ./removeseqscommand.o
1052 # Item # 76 -- systemcommand --
1053 ./systemcommand.o : systemcommand.cpp
1054 $(CC) $(CC_OPTIONS) systemcommand.cpp -c $(INCLUDE) -o ./systemcommand.o
1057 # Item # 77 -- binsequencecommand --
1058 ./binsequencecommand.o : binsequencecommand.cpp
1059 $(CC) $(CC_OPTIONS) binsequencecommand.cpp -c $(INCLUDE) -o ./binsequencecommand.o
1062 # Item # 78 -- distancecommand --
1063 ./distancecommand.o : distancecommand.cpp
1064 $(CC) $(CC_OPTIONS) distancecommand.cpp -c $(INCLUDE) -o ./distancecommand.o
1067 # Item # 79 -- ace --
1069 $(CC) $(CC_OPTIONS) ace.cpp -c $(INCLUDE) -o ./ace.o
1072 # Item # 80 -- averagelinkage --
1073 ./averagelinkage.o : averagelinkage.cpp
1074 $(CC) $(CC_OPTIONS) averagelinkage.cpp -c $(INCLUDE) -o ./averagelinkage.o
1077 # Item # 81 -- bootstrap --
1078 ./bootstrap.o : bootstrap.cpp
1079 $(CC) $(CC_OPTIONS) bootstrap.cpp -c $(INCLUDE) -o ./bootstrap.o
1082 # Item # 82 -- calculator --
1083 ./calculator.o : calculator.cpp
1084 $(CC) $(CC_OPTIONS) calculator.cpp -c $(INCLUDE) -o ./calculator.o
1087 # Item # 83 -- chao1 --
1088 ./chao1.o : chao1.cpp
1089 $(CC) $(CC_OPTIONS) chao1.cpp -c $(INCLUDE) -o ./chao1.o
1092 # Item # 84 -- cluster --
1093 ./cluster.o : cluster.cpp
1094 $(CC) $(CC_OPTIONS) cluster.cpp -c $(INCLUDE) -o ./cluster.o
1097 # Item # 85 -- clustercommand --
1098 ./clustercommand.o : clustercommand.cpp
1099 $(CC) $(CC_OPTIONS) clustercommand.cpp -c $(INCLUDE) -o ./clustercommand.o
1102 # Item # 86 -- collect --
1103 ./collect.o : collect.cpp
1104 $(CC) $(CC_OPTIONS) collect.cpp -c $(INCLUDE) -o ./collect.o
1107 # Item # 87 -- collectcommand --
1108 ./collectcommand.o : collectcommand.cpp
1109 $(CC) $(CC_OPTIONS) collectcommand.cpp -c $(INCLUDE) -o ./collectcommand.o
1112 # Item # 88 -- collectsharedcommand --
1113 ./collectsharedcommand.o : collectsharedcommand.cpp
1114 $(CC) $(CC_OPTIONS) collectsharedcommand.cpp -c $(INCLUDE) -o ./collectsharedcommand.o
1117 # Item # 89 -- commandoptionparser --
1118 ./commandoptionparser.o : commandoptionparser.cpp
1119 $(CC) $(CC_OPTIONS) commandoptionparser.cpp -c $(INCLUDE) -o ./commandoptionparser.o
1122 # Item # 90 -- completelinkage --
1123 ./completelinkage.o : completelinkage.cpp
1124 $(CC) $(CC_OPTIONS) completelinkage.cpp -c $(INCLUDE) -o ./completelinkage.o
1127 # Item # 91 -- database --
1128 ./database.o : database.cpp
1129 $(CC) $(CC_OPTIONS) database.cpp -c $(INCLUDE) -o ./database.o
1132 # Item # 92 -- engine --
1133 ./engine.o : engine.cpp
1134 $(CC) $(CC_OPTIONS) engine.cpp -c $(INCLUDE) -o ./engine.o
1137 # Item # 93 -- fastamap --
1138 ./fastamap.o : fastamap.cpp
1139 $(CC) $(CC_OPTIONS) fastamap.cpp -c $(INCLUDE) -o ./fastamap.o
1142 # Item # 94 -- fileoutput --
1143 ./fileoutput.o : fileoutput.cpp
1144 $(CC) $(CC_OPTIONS) fileoutput.cpp -c $(INCLUDE) -o ./fileoutput.o
1147 # Item # 95 -- globaldata --
1148 ./globaldata.o : globaldata.cpp
1149 $(CC) $(CC_OPTIONS) globaldata.cpp -c $(INCLUDE) -o ./globaldata.o
1152 # Item # 96 -- groupmap --
1153 ./groupmap.o : groupmap.cpp
1154 $(CC) $(CC_OPTIONS) groupmap.cpp -c $(INCLUDE) -o ./groupmap.o
1157 # Item # 97 -- helpcommand --
1158 ./helpcommand.o : helpcommand.cpp
1159 $(CC) $(CC_OPTIONS) helpcommand.cpp -c $(INCLUDE) -o ./helpcommand.o
1162 # Item # 98 -- inputdata --
1163 ./inputdata.o : inputdata.cpp
1164 $(CC) $(CC_OPTIONS) inputdata.cpp -c $(INCLUDE) -o ./inputdata.o
1167 # Item # 99 -- jackknife --
1168 ./jackknife.o : jackknife.cpp
1169 $(CC) $(CC_OPTIONS) jackknife.cpp -c $(INCLUDE) -o ./jackknife.o
1172 # Item # 100 -- kmer --
1174 $(CC) $(CC_OPTIONS) kmer.cpp -c $(INCLUDE) -o ./kmer.o
1177 # Item # 101 -- kmerdb --
1178 ./kmerdb.o : kmerdb.cpp
1179 $(CC) $(CC_OPTIONS) kmerdb.cpp -c $(INCLUDE) -o ./kmerdb.o
1182 # Item # 102 -- listvector --
1183 ./listvector.o : listvector.cpp
1184 $(CC) $(CC_OPTIONS) listvector.cpp -c $(INCLUDE) -o ./listvector.o
1187 # Item # 103 -- mothur --
1188 ./mothur.o : mothur.cpp
1189 $(CC) $(CC_OPTIONS) mothur.cpp -c $(INCLUDE) -o ./mothur.o
1192 # Item # 104 -- nameassignment --
1193 ./nameassignment.o : nameassignment.cpp
1194 $(CC) $(CC_OPTIONS) nameassignment.cpp -c $(INCLUDE) -o ./nameassignment.o
1197 # Item # 105 -- npshannon --
1198 ./npshannon.o : npshannon.cpp
1199 $(CC) $(CC_OPTIONS) npshannon.cpp -c $(INCLUDE) -o ./npshannon.o
1202 # Item # 106 -- ordervector --
1203 ./ordervector.o : ordervector.cpp
1204 $(CC) $(CC_OPTIONS) ordervector.cpp -c $(INCLUDE) -o ./ordervector.o
1207 # Item # 107 -- progress --
1208 ./progress.o : progress.cpp
1209 $(CC) $(CC_OPTIONS) progress.cpp -c $(INCLUDE) -o ./progress.o
1212 # Item # 108 -- quitcommand --
1213 ./quitcommand.o : quitcommand.cpp
1214 $(CC) $(CC_OPTIONS) quitcommand.cpp -c $(INCLUDE) -o ./quitcommand.o
1217 # Item # 109 -- rabundvector --
1218 ./rabundvector.o : rabundvector.cpp
1219 $(CC) $(CC_OPTIONS) rabundvector.cpp -c $(INCLUDE) -o ./rabundvector.o
1222 # Item # 110 -- rarecalc --
1223 ./rarecalc.o : rarecalc.cpp
1224 $(CC) $(CC_OPTIONS) rarecalc.cpp -c $(INCLUDE) -o ./rarecalc.o
1227 # Item # 111 -- raredisplay --
1228 ./raredisplay.o : raredisplay.cpp
1229 $(CC) $(CC_OPTIONS) raredisplay.cpp -c $(INCLUDE) -o ./raredisplay.o
1232 # Item # 112 -- rarefact --
1233 ./rarefact.o : rarefact.cpp
1234 $(CC) $(CC_OPTIONS) rarefact.cpp -c $(INCLUDE) -o ./rarefact.o
1237 # Item # 113 -- rarefactcommand --
1238 ./rarefactcommand.o : rarefactcommand.cpp
1239 $(CC) $(CC_OPTIONS) rarefactcommand.cpp -c $(INCLUDE) -o ./rarefactcommand.o
1242 # Item # 114 -- rarefactsharedcommand --
1243 ./rarefactsharedcommand.o : rarefactsharedcommand.cpp
1244 $(CC) $(CC_OPTIONS) rarefactsharedcommand.cpp -c $(INCLUDE) -o ./rarefactsharedcommand.o
1247 # Item # 115 -- sabundvector --
1248 ./sabundvector.o : sabundvector.cpp
1249 $(CC) $(CC_OPTIONS) sabundvector.cpp -c $(INCLUDE) -o ./sabundvector.o
1252 # Item # 116 -- sequence --
1253 ./sequence.o : sequence.cpp
1254 $(CC) $(CC_OPTIONS) sequence.cpp -c $(INCLUDE) -o ./sequence.o
1257 # Item # 117 -- shannon --
1258 ./shannon.o : shannon.cpp
1259 $(CC) $(CC_OPTIONS) shannon.cpp -c $(INCLUDE) -o ./shannon.o
1262 # Item # 118 -- sharedace --
1263 ./sharedace.o : sharedace.cpp
1264 $(CC) $(CC_OPTIONS) sharedace.cpp -c $(INCLUDE) -o ./sharedace.o
1267 # Item # 119 -- sharedchao1 --
1268 ./sharedchao1.o : sharedchao1.cpp
1269 $(CC) $(CC_OPTIONS) sharedchao1.cpp -c $(INCLUDE) -o ./sharedchao1.o
1272 # Item # 120 -- sharedcommand --
1273 ./sharedcommand.o : sharedcommand.cpp
1274 $(CC) $(CC_OPTIONS) sharedcommand.cpp -c $(INCLUDE) -o ./sharedcommand.o
1277 # Item # 121 -- sharedjabund --
1278 ./sharedjabund.o : sharedjabund.cpp
1279 $(CC) $(CC_OPTIONS) sharedjabund.cpp -c $(INCLUDE) -o ./sharedjabund.o
1282 # Item # 122 -- sharedjclass --
1283 ./sharedjclass.o : sharedjclass.cpp
1284 $(CC) $(CC_OPTIONS) sharedjclass.cpp -c $(INCLUDE) -o ./sharedjclass.o
1287 # Item # 123 -- sharedjest --
1288 ./sharedjest.o : sharedjest.cpp
1289 $(CC) $(CC_OPTIONS) sharedjest.cpp -c $(INCLUDE) -o ./sharedjest.o
1292 # Item # 124 -- sharedordervector --
1293 ./sharedordervector.o : sharedordervector.cpp
1294 $(CC) $(CC_OPTIONS) sharedordervector.cpp -c $(INCLUDE) -o ./sharedordervector.o
1297 # Item # 125 -- sharedrabundvector --
1298 ./sharedrabundvector.o : sharedrabundvector.cpp
1299 $(CC) $(CC_OPTIONS) sharedrabundvector.cpp -c $(INCLUDE) -o ./sharedrabundvector.o
1302 # Item # 126 -- sharedsabundvector --
1303 ./sharedsabundvector.o : sharedsabundvector.cpp
1304 $(CC) $(CC_OPTIONS) sharedsabundvector.cpp -c $(INCLUDE) -o ./sharedsabundvector.o
1307 # Item # 127 -- sharedsobs --
1308 ./sharedsobs.o : sharedsobs.cpp
1309 $(CC) $(CC_OPTIONS) sharedsobs.cpp -c $(INCLUDE) -o ./sharedsobs.o
1312 # Item # 128 -- sharedsorabund --
1313 ./sharedsorabund.o : sharedsorabund.cpp
1314 $(CC) $(CC_OPTIONS) sharedsorabund.cpp -c $(INCLUDE) -o ./sharedsorabund.o
1317 # Item # 129 -- sharedsorclass --
1318 ./sharedsorclass.o : sharedsorclass.cpp
1319 $(CC) $(CC_OPTIONS) sharedsorclass.cpp -c $(INCLUDE) -o ./sharedsorclass.o
1322 # Item # 130 -- sharedsorest --
1323 ./sharedsorest.o : sharedsorest.cpp
1324 $(CC) $(CC_OPTIONS) sharedsorest.cpp -c $(INCLUDE) -o ./sharedsorest.o
1327 # Item # 131 -- sharedthetan --
1328 ./sharedthetan.o : sharedthetan.cpp
1329 $(CC) $(CC_OPTIONS) sharedthetan.cpp -c $(INCLUDE) -o ./sharedthetan.o
1332 # Item # 132 -- sharedthetayc --
1333 ./sharedthetayc.o : sharedthetayc.cpp
1334 $(CC) $(CC_OPTIONS) sharedthetayc.cpp -c $(INCLUDE) -o ./sharedthetayc.o
1337 # Item # 133 -- simpson --
1338 ./simpson.o : simpson.cpp
1339 $(CC) $(CC_OPTIONS) simpson.cpp -c $(INCLUDE) -o ./simpson.o
1342 # Item # 134 -- singlelinkage --
1343 ./singlelinkage.o : singlelinkage.cpp
1344 $(CC) $(CC_OPTIONS) singlelinkage.cpp -c $(INCLUDE) -o ./singlelinkage.o
1347 # Item # 135 -- sparsematrix --
1348 ./sparsematrix.o : sparsematrix.cpp
1349 $(CC) $(CC_OPTIONS) sparsematrix.cpp -c $(INCLUDE) -o ./sparsematrix.o
1352 # Item # 136 -- summarycommand --
1353 ./summarycommand.o : summarycommand.cpp
1354 $(CC) $(CC_OPTIONS) summarycommand.cpp -c $(INCLUDE) -o ./summarycommand.o
1357 # Item # 137 -- summarysharedcommand --
1358 ./summarysharedcommand.o : summarysharedcommand.cpp
1359 $(CC) $(CC_OPTIONS) summarysharedcommand.cpp -c $(INCLUDE) -o ./summarysharedcommand.o
1362 # Item # 138 -- uvest --
1363 ./uvest.o : uvest.cpp
1364 $(CC) $(CC_OPTIONS) uvest.cpp -c $(INCLUDE) -o ./uvest.o
1367 # Item # 139 -- validcalculator --
1368 ./validcalculator.o : validcalculator.cpp
1369 $(CC) $(CC_OPTIONS) validcalculator.cpp -c $(INCLUDE) -o ./validcalculator.o
1372 # Item # 140 -- validparameter --
1373 ./validparameter.o : validparameter.cpp
1374 $(CC) $(CC_OPTIONS) validparameter.cpp -c $(INCLUDE) -o ./validparameter.o
1377 # Item # 141 -- treenode --
1378 ./treenode.o : treenode.cpp
1379 $(CC) $(CC_OPTIONS) treenode.cpp -c $(INCLUDE) -o ./treenode.o
1382 # Item # 142 -- readtreecommand --
1383 ./readtreecommand.o : readtreecommand.cpp
1384 $(CC) $(CC_OPTIONS) readtreecommand.cpp -c $(INCLUDE) -o ./readtreecommand.o
1387 # Item # 143 -- reversecommand --
1388 ./reversecommand.o : reversecommand.cpp
1389 $(CC) $(CC_OPTIONS) reversecommand.cpp -c $(INCLUDE) -o ./reversecommand.o
1392 # Item # 144 -- trimseqscommand --
1393 ./trimseqscommand.o : trimseqscommand.cpp
1394 $(CC) $(CC_OPTIONS) trimseqscommand.cpp -c $(INCLUDE) -o ./trimseqscommand.o
1397 # Item # 145 -- slibshuff --
1398 ./slibshuff.o : slibshuff.cpp
1399 $(CC) $(CC_OPTIONS) slibshuff.cpp -c $(INCLUDE) -o ./slibshuff.o
1402 # Item # 146 -- libshuff --
1403 ./libshuff.o : libshuff.cpp
1404 $(CC) $(CC_OPTIONS) libshuff.cpp -c $(INCLUDE) -o ./libshuff.o
1407 # Item # 147 -- dlibshuff --
1408 ./dlibshuff.o : dlibshuff.cpp
1409 $(CC) $(CC_OPTIONS) dlibshuff.cpp -c $(INCLUDE) -o ./dlibshuff.o
1412 # Item # 148 -- mergefilecommand --
1413 ./mergefilecommand.o : mergefilecommand.cpp
1414 $(CC) $(CC_OPTIONS) mergefilecommand.cpp -c $(INCLUDE) -o ./mergefilecommand.o
1417 # Item # 149 -- coverage --
1418 ./coverage.o : coverage.cpp
1419 $(CC) $(CC_OPTIONS) coverage.cpp -c $(INCLUDE) -o ./coverage.o
1422 # Item # 150 -- whittaker --
1423 ./whittaker.o : whittaker.cpp
1424 $(CC) $(CC_OPTIONS) whittaker.cpp -c $(INCLUDE) -o ./whittaker.o
1427 # Item # 151 -- preclustercommand --
1428 ./preclustercommand.o : preclustercommand.cpp
1429 $(CC) $(CC_OPTIONS) preclustercommand.cpp -c $(INCLUDE) -o ./preclustercommand.o
1432 # Item # 152 -- otuhierarchycommand --
1433 ./otuhierarchycommand.o : otuhierarchycommand.cpp
1434 $(CC) $(CC_OPTIONS) otuhierarchycommand.cpp -c $(INCLUDE) -o ./otuhierarchycommand.o
1437 # Item # 153 -- setdircommand --
1438 ./setdircommand.o : setdircommand.cpp
1439 $(CC) $(CC_OPTIONS) setdircommand.cpp -c $(INCLUDE) -o ./setdircommand.o
1442 # Item # 154 -- getgroupcommand --
1443 ./getgroupcommand.o : getgroupcommand.cpp
1444 $(CC) $(CC_OPTIONS) getgroupcommand.cpp -c $(INCLUDE) -o ./getgroupcommand.o
1447 # Item # 155 -- getlabelcommand --
1448 ./getlabelcommand.o : getlabelcommand.cpp
1449 $(CC) $(CC_OPTIONS) getlabelcommand.cpp -c $(INCLUDE) -o ./getlabelcommand.o
1452 # Item # 156 -- secondarystructurecommand --
1453 ./secondarystructurecommand.o : secondarystructurecommand.cpp
1454 $(CC) $(CC_OPTIONS) secondarystructurecommand.cpp -c $(INCLUDE) -o ./secondarystructurecommand.o
1457 # Item # 157 -- mothurout --
1458 ./mothurout.o : mothurout.cpp
1459 $(CC) $(CC_OPTIONS) mothurout.cpp -c $(INCLUDE) -o ./mothurout.o
1462 # Item # 158 -- parselistscommand --
1463 ./parselistscommand.o : parselistscommand.cpp
1464 $(CC) $(CC_OPTIONS) parselistscommand.cpp -c $(INCLUDE) -o ./parselistscommand.o
1467 # Item # 159 -- readblast --
1468 ./readblast.o : readblast.cpp
1469 $(CC) $(CC_OPTIONS) readblast.cpp -c $(INCLUDE) -o ./readblast.o
1472 # Item # 160 -- chimeracheckrdp --
1473 ./chimeracheckrdp.o : chimeracheckrdp.cpp
1474 $(CC) $(CC_OPTIONS) chimeracheckrdp.cpp -c $(INCLUDE) -o ./chimeracheckrdp.o
1477 # Item # 161 -- hclustercommand --
1478 ./hclustercommand.o : hclustercommand.cpp
1479 $(CC) $(CC_OPTIONS) hclustercommand.cpp -c $(INCLUDE) -o ./hclustercommand.o
1482 # Item # 162 -- hcluster --
1483 ./hcluster.o : hcluster.cpp
1484 $(CC) $(CC_OPTIONS) hcluster.cpp -c $(INCLUDE) -o ./hcluster.o
1487 # Item # 163 -- getlistcountcommand --
1488 ./getlistcountcommand.o : getlistcountcommand.cpp
1489 $(CC) $(CC_OPTIONS) getlistcountcommand.cpp -c $(INCLUDE) -o ./getlistcountcommand.o
1492 # Item # 164 -- readcluster --
1493 ./readcluster.o : readcluster.cpp
1494 $(CC) $(CC_OPTIONS) readcluster.cpp -c $(INCLUDE) -o ./readcluster.o
1497 # Item # 165 -- ccode --
1498 ./ccode.o : ccode.cpp
1499 $(CC) $(CC_OPTIONS) ccode.cpp -c $(INCLUDE) -o ./ccode.o
1502 # Item # 166 -- taxonomyequalizer --
1503 ./taxonomyequalizer.o : taxonomyequalizer.cpp
1504 $(CC) $(CC_OPTIONS) taxonomyequalizer.cpp -c $(INCLUDE) -o ./taxonomyequalizer.o
1507 # Item # 167 -- phylotypecommand --
1508 ./phylotypecommand.o : phylotypecommand.cpp
1509 $(CC) $(CC_OPTIONS) phylotypecommand.cpp -c $(INCLUDE) -o ./phylotypecommand.o
1512 # Item # 168 -- classifyseqscommand --
1513 ./classifyseqscommand.o : classifyseqscommand.cpp
1514 $(CC) $(CC_OPTIONS) classifyseqscommand.cpp -c $(INCLUDE) -o ./classifyseqscommand.o
1517 # Item # 169 -- classify --
1518 ./classify.o : classify.cpp
1519 $(CC) $(CC_OPTIONS) classify.cpp -c $(INCLUDE) -o ./classify.o
1522 # Item # 170 -- phylotree --
1523 ./phylotree.o : phylotree.cpp
1524 $(CC) $(CC_OPTIONS) phylotree.cpp -c $(INCLUDE) -o ./phylotree.o
1527 # Item # 171 -- bayesian --
1528 ./bayesian.o : bayesian.cpp
1529 $(CC) $(CC_OPTIONS) bayesian.cpp -c $(INCLUDE) -o ./bayesian.o
1532 # Item # 172 -- alignmentdb --
1533 ./alignmentdb.o : alignmentdb.cpp
1534 $(CC) $(CC_OPTIONS) alignmentdb.cpp -c $(INCLUDE) -o ./alignmentdb.o
1537 # Item # 173 -- knn --
1539 $(CC) $(CC_OPTIONS) knn.cpp -c $(INCLUDE) -o ./knn.o
1542 # Item # 174 -- distancedb --
1543 ./distancedb.o : distancedb.cpp
1544 $(CC) $(CC_OPTIONS) distancedb.cpp -c $(INCLUDE) -o ./distancedb.o
1547 # Item # 175 -- chimeraslayer --
1548 ./chimeraslayer.o : chimeraslayer.cpp
1549 $(CC) $(CC_OPTIONS) chimeraslayer.cpp -c $(INCLUDE) -o ./chimeraslayer.o
1552 # Item # 176 -- slayer --
1553 ./slayer.o : slayer.cpp
1554 $(CC) $(CC_OPTIONS) slayer.cpp -c $(INCLUDE) -o ./slayer.o
1557 # Item # 177 -- pcacommand --
1558 ./pcacommand.o : pcacommand.cpp
1559 $(CC) $(CC_OPTIONS) pcacommand.cpp -c $(INCLUDE) -o ./pcacommand.o
1562 # Item # 178 -- formatcolumn --
1563 ./formatcolumn.o : formatcolumn.cpp
1564 $(CC) $(CC_OPTIONS) formatcolumn.cpp -c $(INCLUDE) -o ./formatcolumn.o
1567 # Item # 179 -- formatphylip --
1568 ./formatphylip.o : formatphylip.cpp
1569 $(CC) $(CC_OPTIONS) formatphylip.cpp -c $(INCLUDE) -o ./formatphylip.o
1572 # Item # 180 -- mgclustercommand --
1573 ./mgclustercommand.o : mgclustercommand.cpp
1574 $(CC) $(CC_OPTIONS) mgclustercommand.cpp -c $(INCLUDE) -o ./mgclustercommand.o
1577 # Item # 181 -- getsharedotucommand --
1578 ./getsharedotucommand.o : getsharedotucommand.cpp
1579 $(CC) $(CC_OPTIONS) getsharedotucommand.cpp -c $(INCLUDE) -o ./getsharedotucommand.o
1582 # Item # 182 -- maligner --
1583 ./maligner.o : maligner.cpp
1584 $(CC) $(CC_OPTIONS) maligner.cpp -c $(INCLUDE) -o ./maligner.o
1587 # Item # 183 -- chimerarealigner --
1588 ./chimerarealigner.o : chimerarealigner.cpp
1589 $(CC) $(CC_OPTIONS) chimerarealigner.cpp -c $(INCLUDE) -o ./chimerarealigner.o
1592 # Item # 184 -- bergerparker --
1593 ./bergerparker.o : bergerparker.cpp
1594 $(CC) $(CC_OPTIONS) bergerparker.cpp -c $(INCLUDE) -o ./bergerparker.o
1597 # Item # 185 -- bstick --
1598 ./bstick.o : bstick.cpp
1599 $(CC) $(CC_OPTIONS) bstick.cpp -c $(INCLUDE) -o ./bstick.o
1602 # Item # 186 -- sharedkstest --
1603 ./sharedkstest.o : sharedkstest.cpp
1604 $(CC) $(CC_OPTIONS) sharedkstest.cpp -c $(INCLUDE) -o ./sharedkstest.o
1607 # Item # 187 -- qstat --
1608 ./qstat.o : qstat.cpp
1609 $(CC) $(CC_OPTIONS) qstat.cpp -c $(INCLUDE) -o ./qstat.o
1612 # Item # 188 -- shen --
1614 $(CC) $(CC_OPTIONS) shen.cpp -c $(INCLUDE) -o ./shen.o
1617 # Item # 189 -- logsd --
1618 ./logsd.o : logsd.cpp
1619 $(CC) $(CC_OPTIONS) logsd.cpp -c $(INCLUDE) -o ./logsd.o
1622 # Item # 190 -- geom --
1624 $(CC) $(CC_OPTIONS) geom.cpp -c $(INCLUDE) -o ./geom.o
1626 # Item # 191 -- parsesffcommand --
1627 ./parsesffcommand.o : parsesffcommand.cpp
1628 $(CC) $(CC_OPTIONS) parsesffcommand.cpp -c $(INCLUDE) -o ./parsesffcommand.o
1630 # Item # 192 -- chimeraccodecommand --
1631 ./chimeraccodecommand.o : chimeraccodecommand.cpp
1632 $(CC) $(CC_OPTIONS) chimeraccodecommand.cpp -c $(INCLUDE) -o ./chimeraccodecommand.o
1634 # Item # 193 -- chimeracheckcommand --
1635 ./chimeracheckcommand.o : chimeracheckcommand.cpp
1636 $(CC) $(CC_OPTIONS) chimeracheckcommand.cpp -c $(INCLUDE) -o ./chimeracheckcommand.o
1639 # Item # 194 -- chimeraslayercommand --
1640 ./chimeraslayercommand.o : chimeraslayercommand.cpp
1641 $(CC) $(CC_OPTIONS) chimeraslayercommand.cpp -c $(INCLUDE) -o ./chimeraslayercommand.o
1643 # Item # 195 -- chimerapintailcommand --
1644 ./chimerapintailcommand.o : chimerapintailcommand.cpp
1645 $(CC) $(CC_OPTIONS) chimerapintailcommand.cpp -c $(INCLUDE) -o ./chimerapintailcommand.o
1647 # Item # 196 -- chimerabellerophoncommand --
1648 ./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp
1649 $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o
1651 # Item # 197 -- phylosummary --
1652 ./phylosummary.o : phylosummary.cpp
1653 $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o
1655 # Item # 198 -- setlogfilecommand --
1656 ./setlogfilecommand.o : setlogfilecommand.cpp
1657 $(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o
1659 # Item # 199 -- phylodiversity --
1660 ./phylodiversity.o : phylodiversity.cpp
1661 $(CC) $(CC_OPTIONS) phylodiversity.cpp -c $(INCLUDE) -o ./phylodiversity.o
1663 # Item # 200 -- phylodiversitycommand --
1664 ./phylodiversitycommand.o : phylodiversitycommand.cpp
1665 $(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o
1667 # Item # 201 -- makegroupcommand --
1668 ./makegroupcommand.o : makegroupcommand.cpp
1669 $(CC) $(CC_OPTIONS) makegroupcommand.cpp -c $(INCLUDE) -o ./makegroupcommand.o
1671 # Item # 202 -- chopseqscommand --
1672 ./chopseqscommand.o : chopseqscommand.cpp
1673 $(CC) $(CC_OPTIONS) chopseqscommand.cpp -c $(INCLUDE) -o ./chopseqscommand.o
1675 # Item # 203 -- clearcutcommand --
1676 ./clearcutcommand.o : clearcutcommand.cpp
1677 $(CC) $(CC_OPTIONS) clearcutcommand.cpp -c $(INCLUDE) -o ./clearcutcommand.o
1679 # Item # 204 -- catchallcommand --
1680 ./catchallcommand.o : catchallcommand.cpp
1681 $(CC) $(CC_OPTIONS) catchallcommand.cpp -c $(INCLUDE) -o ./catchallcommand.o
1683 # Item # 205 -- catchallcommand --
1684 ./splitabundcommand : splitabundcommand
1685 $(CC) $(CC_OPTIONS) splitabundcommand -c $(INCLUDE) -o ./splitabundcommand