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mothur 1.48.1-1
  • links: PTS, VCS
  • area: main
  • in suites: forky, sid, trixie
  • size: 13,692 kB
  • sloc: cpp: 161,866; makefile: 122; sh: 31

Folder: commands

d .. (parent)
- - rwxr-xr-x 14,487 aligncheckcommand.cpp
- - rwxr-xr-x 1,617 aligncheckcommand.h
- - rw-r--r-- 28,273 aligncommand.cpp
- - rwxr-xr-x 2,034 aligncommand.h
- - rw-r--r-- 16,359 alignmusclecommand.cpp
- - rw-r--r-- 1,569 alignmusclecommand.hpp
- - rwxr-xr-x 16,438 amovacommand.cpp
- - rwxr-xr-x 1,355 amovacommand.h
- - rwxr-xr-x 15,436 anosimcommand.cpp
- - rwxr-xr-x 1,453 anosimcommand.h
- - rw-r--r-- 14,712 binsequencecommand.cpp
- - rwxr-xr-x 1,242 binsequencecommand.h
- - rw-r--r-- 18,157 biominfocommand.cpp
- - rwxr-xr-x 1,624 biominfocommand.h
- - rwxr-xr-x 10,727 chimerabellerophoncommand.cpp
- - rwxr-xr-x 1,313 chimerabellerophoncommand.h
- - rwxr-xr-x 14,315 chimeraccodecommand.cpp
- - rwxr-xr-x 1,325 chimeraccodecommand.h
- - rwxr-xr-x 9,764 chimeracheckcommand.cpp
- - rwxr-xr-x 1,268 chimeracheckcommand.h
- - rw-r--r-- 46,302 chimeraperseuscommand.cpp
- - rwxr-xr-x 1,783 chimeraperseuscommand.h
- - rwxr-xr-x 19,322 chimerapintailcommand.cpp
- - rwxr-xr-x 1,693 chimerapintailcommand.h
- - rwxr-xr-x 47,154 chimeraslayercommand.cpp
- - rwxr-xr-x 2,283 chimeraslayercommand.h
- - rw-r--r-- 70,096 chimerauchimecommand.cpp
- - rwxr-xr-x 4,057 chimerauchimecommand.h
- - rw-r--r-- 63,623 chimeravsearchcommand.cpp
- - rwxr-xr-x 4,092 chimeravsearchcommand.h
- - rwxr-xr-x 37,987 chopseqscommand.cpp
- - rwxr-xr-x 1,283 chopseqscommand.h
- - rwxr-xr-x 33,293 classifyotucommand.cpp
- - rwxr-xr-x 1,650 classifyotucommand.h
- - rw-r--r-- 34,722 classifyseqscommand.cpp
- - rw-r--r-- 2,648 classifyseqscommand.h
- - rwxr-xr-x 28,926 classifysvmsharedcommand.cpp
- - rwxr-xr-x 2,485 classifysvmsharedcommand.h
- - rwxr-xr-x 19,759 classifytreecommand.cpp
- - rwxr-xr-x 1,370 classifytreecommand.h
- - rwxr-xr-x 16,341 clearcutcommand.cpp
- - rwxr-xr-x 1,482 clearcutcommand.h
- - rw-r--r-- 49,184 clustercommand.cpp
- - rwxr-xr-x 2,841 clustercommand.h
- - rwxr-xr-x 12,795 clusterdoturcommand.cpp
- - rwxr-xr-x 1,649 clusterdoturcommand.h
- - rw-r--r-- 70,311 clusterfitcommand.cpp
- - rwxr-xr-x 2,865 clusterfitcommand.hpp
- - rwxr-xr-x 15,647 clusterfragmentscommand.cpp
- - rwxr-xr-x 1,902 clusterfragmentscommand.h
- - rw-r--r-- 78,687 clustersplitcommand.cpp
- - rwxr-xr-x 2,384 clustersplitcommand.h
- - rwxr-xr-x 27,470 collectcommand.cpp
- - rwxr-xr-x 2,343 collectcommand.h
- - rwxr-xr-x 30,482 collectsharedcommand.cpp
- - rwxr-xr-x 1,402 collectsharedcommand.h
- - rwxr-xr-x 7,301 command.hpp
- - rwxr-xr-x 28,313 consensusseqscommand.cpp
- - rwxr-xr-x 1,318 consensusseqscommand.h
- - rwxr-xr-x 21,044 cooccurrencecommand.cpp
- - rwxr-xr-x 1,314 cooccurrencecommand.h
- - rw-r--r-- 30,921 corraxescommand.cpp
- - rwxr-xr-x 1,683 corraxescommand.h
- - rwxr-xr-x 11,600 countgroupscommand.cpp
- - rwxr-xr-x 936 countgroupscommand.h
- - rwxr-xr-x 18,093 countseqscommand.cpp
- - rwxr-xr-x 1,252 countseqscommand.h
- - rwxr-xr-x 37,740 createdatabasecommand.cpp
- - rwxr-xr-x 1,435 createdatabasecommand.h
- - rwxr-xr-x 10,967 degapseqscommand.cpp
- - rwxr-xr-x 960 degapseqscommand.h
- - rwxr-xr-x 11,065 deuniqueseqscommand.cpp
- - rwxr-xr-x 1,003 deuniqueseqscommand.h
- - rwxr-xr-x 5,919 deuniquetreecommand.cpp
- - rwxr-xr-x 1,016 deuniquetreecommand.h
- - rw-r--r-- 40,946 distancecommand.cpp
- - rwxr-xr-x 2,944 distancecommand.h
- - rwxr-xr-x 32,626 distsharedcommand.cpp
- - rwxr-xr-x 4,001 distsharedcommand.h
- - rw-r--r-- 44,827 diversityestimatorcommand.cpp
- - rw-r--r-- 2,402 diversityestimatorcommand.hpp
- - rwxr-xr-x 57,798 fastaqinfocommand.cpp
- - rw-r--r-- 2,374 fastaqinfocommand.h
- - rw-r--r-- 24,164 filterseqscommand.cpp
- - rwxr-xr-x 3,285 filterseqscommand.h
- - rwxr-xr-x 20,035 filtersharedcommand.cpp
- - rwxr-xr-x 1,198 filtersharedcommand.h
- - rwxr-xr-x 17,790 getcoremicrobiomecommand.cpp
- - rwxr-xr-x 1,643 getcoremicrobiomecommand.h
- - rwxr-xr-x 8,810 getcurrentcommand.cpp
- - rwxr-xr-x 928 getcurrentcommand.h
- - rwxr-xr-x 14,787 getdistscommand.cpp
- - rwxr-xr-x 1,030 getdistscommand.h
- - rwxr-xr-x 4,069 getgroupcommand.cpp
- - rwxr-xr-x 901 getgroupcommand.h
- - rwxr-xr-x 46,222 getgroupscommand.cpp
- - rwxr-xr-x 1,767 getgroupscommand.h
- - rwxr-xr-x 5,433 getlabelcommand.cpp
- - rwxr-xr-x 936 getlabelcommand.h
- - rw-r--r-- 25,477 getlineagecommand.cpp
- - rwxr-xr-x 1,353 getlineagecommand.h
- - rwxr-xr-x 7,946 getlistcountcommand.cpp
- - rwxr-xr-x 1,176 getlistcountcommand.h
- - rw-r--r-- 40,939 getmetacommunitycommand.cpp
- - rwxr-xr-x 3,451 getmetacommunitycommand.h
- - rwxr-xr-x 165,201 getmimarkspackagecommand.cpp
- - rwxr-xr-x 1,411 getmimarkspackagecommand.h
- - rw-r--r-- 49,338 getoturepcommand.cpp
- - rwxr-xr-x 2,455 getoturepcommand.h
- - rwxr-xr-x 24,111 getotuscommand.cpp
- - rwxr-xr-x 1,552 getotuscommand.h
- - rwxr-xr-x 12,280 getrabundcommand.cpp
- - rwxr-xr-x 1,182 getrabundcommand.h
- - rwxr-xr-x 9,888 getrelabundcommand.cpp
- - rwxr-xr-x 1,096 getrelabundcommand.h
- - rwxr-xr-x 10,504 getsabundcommand.cpp
- - rwxr-xr-x 1,165 getsabundcommand.h
- - rw-r--r-- 64,354 getseqscommand.cpp
- - rwxr-xr-x 3,619 getseqscommand.h
- - rwxr-xr-x 26,249 getsharedotucommand.cpp
- - rwxr-xr-x 1,778 getsharedotucommand.h
- - rwxr-xr-x 13,686 heatmapcommand.cpp
- - rwxr-xr-x 1,190 heatmapcommand.h
- - rwxr-xr-x 18,868 heatmapsimcommand.cpp
- - rwxr-xr-x 1,341 heatmapsimcommand.h
- - rw-r--r-- 35,090 helpcommand.cpp
- - rwxr-xr-x 1,135 helpcommand.h
- - rwxr-xr-x 15,560 homovacommand.cpp
- - rwxr-xr-x 1,355 homovacommand.h
- - rwxr-xr-x 57,384 indicatorcommand.cpp
- - rwxr-xr-x 3,166 indicatorcommand.h
- - rwxr-xr-x 9,792 kruskalwalliscommand.cpp
- - rwxr-xr-x 1,316 kruskalwalliscommand.h
- - rwxr-xr-x 60,954 lefsecommand.cpp
- - rwxr-xr-x 4,855 lefsecommand.h
- - rwxr-xr-x 21,598 libshuffcommand.cpp
- - rwxr-xr-x 1,796 libshuffcommand.h
- - rwxr-xr-x 12,774 listotuscommand.cpp
- - rwxr-xr-x 1,717 listotuscommand.h
- - rwxr-xr-x 19,071 listseqscommand.cpp
- - rwxr-xr-x 1,321 listseqscommand.h
- - rwxr-xr-x 26,124 makebiomcommand.cpp
- - rwxr-xr-x 1,489 makebiomcommand.h
- - rw-r--r-- 9,633 makeclrcommand.cpp
- - rw-r--r-- 1,234 makeclrcommand.hpp
- - rw-r--r-- 152,281 makecontigscommand.cpp
- - rw-r--r-- 4,491 makecontigscommand.h
- - rwxr-xr-x 7,487 makefastqcommand.cpp
- - rwxr-xr-x 923 makefastqcommand.h
- - rwxr-xr-x 22,589 makefilecommand.cpp
- - rwxr-xr-x 1,482 makefilecommand.h
- - rw-r--r-- 12,179 makegroupcommand.cpp
- - rwxr-xr-x 1,050 makegroupcommand.h
- - rwxr-xr-x 21,291 makelefsecommand.cpp
- - rwxr-xr-x 1,531 makelefsecommand.h
- - rwxr-xr-x 32,472 makelookupcommand.cpp
- - rwxr-xr-x 1,782 makelookupcommand.h
- - rwxr-xr-x 55,451 makesharedcommand.cpp
- - rwxr-xr-x 2,392 makesharedcommand.h
- - rwxr-xr-x 8,860 mantelcommand.cpp
- - rwxr-xr-x 1,080 mantelcommand.h
- - rwxr-xr-x 9,154 mergecountcommand.cpp
- - rwxr-xr-x 1,127 mergecountcommand.hpp
- - rwxr-xr-x 13,056 mergefilecommand.cpp
- - rwxr-xr-x 1,028 mergefilecommand.h
- - rwxr-xr-x 25,577 mergegroupscommand.cpp
- - rwxr-xr-x 1,447 mergegroupscommand.h
- - rw-r--r-- 27,515 mergeotuscommand.cpp
- - rw-r--r-- 1,620 mergeotuscommand.hpp
- - rwxr-xr-x 16,959 mergesfffilecommand.cpp
- - rwxr-xr-x 1,396 mergesfffilecommand.h
- - rwxr-xr-x 13,527 mergetaxsummarycommand.cpp
- - rwxr-xr-x 1,315 mergetaxsummarycommand.h
- - rwxr-xr-x 25,588 metastatscommand.cpp
- - rwxr-xr-x 1,753 metastatscommand.h
- - rwxr-xr-x 37,239 mgclustercommand.cpp
- - rwxr-xr-x 2,084 mgclustercommand.h
- - rwxr-xr-x 22,066 mimarksattributescommand.cpp
- - rwxr-xr-x 2,863 mimarksattributescommand.h
- - rwxr-xr-x 15,819 newcommandtemplate.cpp
- - rwxr-xr-x 1,819 newcommandtemplate.h
- - rwxr-xr-x 20,155 nmdscommand.cpp
- - rwxr-xr-x 2,019 nmdscommand.h
- - rwxr-xr-x 856 nocommands.cpp
- - rwxr-xr-x 1,021 nocommands.h
- - rwxr-xr-x 17,493 normalizesharedcommand.cpp
- - rwxr-xr-x 1,196 normalizesharedcommand.h
- - rwxr-xr-x 20,204 otuassociationcommand.cpp
- - rwxr-xr-x 1,299 otuassociationcommand.h
- - rwxr-xr-x 20,389 otuhierarchycommand.cpp
- - rwxr-xr-x 1,455 otuhierarchycommand.h
- - rw-r--r-- 47,919 pairwiseseqscommand.cpp
- - rwxr-xr-x 2,212 pairwiseseqscommand.h
- - rwxr-xr-x 21,148 parsimonycommand.cpp
- - rwxr-xr-x 3,256 parsimonycommand.h
- - rwxr-xr-x 15,439 pcacommand.cpp
- - rwxr-xr-x 1,485 pcacommand.h
- - rwxr-xr-x 8,590 pcoacommand.cpp
- - rwxr-xr-x 1,300 pcoacommand.h
- - rw-r--r-- 53,092 pcrseqscommand.cpp
- - rwxr-xr-x 1,538 pcrseqscommand.h
- - rwxr-xr-x 32,055 phylodiversitycommand.cpp
- - rwxr-xr-x 1,975 phylodiversitycommand.h
- - rwxr-xr-x 13,907 phylotypecommand.cpp
- - rwxr-xr-x 1,278 phylotypecommand.h
- - rw-r--r-- 61,933 preclustercommand.cpp
- - rwxr-xr-x 1,993 preclustercommand.h
- - rwxr-xr-x 51,177 primerdesigncommand.cpp
- - rwxr-xr-x 2,021 primerdesigncommand.h
- - rwxr-xr-x 1,111 quitcommand.cpp
- - rwxr-xr-x 1,068 quitcommand.h
- - rwxr-xr-x 32,891 rarefactcommand.cpp
- - rwxr-xr-x 1,616 rarefactcommand.h
- - rwxr-xr-x 32,221 rarefactsharedcommand.cpp
- - rwxr-xr-x 1,629 rarefactsharedcommand.h
- - rwxr-xr-x 15,211 removedistscommand.cpp
- - rwxr-xr-x 1,056 removedistscommand.h
- - rwxr-xr-x 46,669 removegroupscommand.cpp
- - rwxr-xr-x 1,764 removegroupscommand.h
- - rwxr-xr-x 27,827 removelineagecommand.cpp
- - rwxr-xr-x 1,402 removelineagecommand.h
- - rwxr-xr-x 24,668 removeotuscommand.cpp
- - rwxr-xr-x 1,578 removeotuscommand.h
- - rwxr-xr-x 28,788 removerarecommand.cpp
- - rwxr-xr-x 1,229 removerarecommand.h
- - rwxr-xr-x 45,853 removeseqscommand.cpp
- - rwxr-xr-x 1,945 removeseqscommand.h
- - rwxr-xr-x 26,049 renamefilecommand.cpp
- - rwxr-xr-x 1,491 renamefilecommand.h
- - rwxr-xr-x 45,604 renameseqscommand.cpp
- - rwxr-xr-x 1,607 renameseqscommand.h
- - rwxr-xr-x 8,106 reversecommand.cpp
- - rwxr-xr-x 901 reversecommand.h
- - rw-r--r-- 58,982 screenseqscommand.cpp
- - rwxr-xr-x 3,224 screenseqscommand.h
- - rwxr-xr-x 15,397 sensspeccommand.cpp
- - rwxr-xr-x 1,553 sensspeccommand.h
- - rwxr-xr-x 41,332 seqerrorcommand.cpp
- - rwxr-xr-x 2,682 seqerrorcommand.h
- - rw-r--r-- 17,943 seqsummarycommand.cpp
- - rwxr-xr-x 1,197 seqsummarycommand.h
- - rwxr-xr-x 26,759 setcurrentcommand.cpp
- - rwxr-xr-x 1,273 setcurrentcommand.h
- - rwxr-xr-x 15,771 setdircommand.cpp
- - rwxr-xr-x 1,062 setdircommand.h
- - rwxr-xr-x 3,938 setlogfilecommand.cpp
- - rwxr-xr-x 991 setlogfilecommand.h
- - rw-r--r-- 3,718 setseedcommand.cpp
- - rwxr-xr-x 1,079 setseedcommand.h
- - rwxr-xr-x 45,973 sffinfocommand.cpp
- - rwxr-xr-x 2,478 sffinfocommand.h
- - rwxr-xr-x 46,598 sffmultiplecommand.cpp
- - rwxr-xr-x 1,604 sffmultiplecommand.h
- - rwxr-xr-x 71,159 shhhercommand.cpp
- - rwxr-xr-x 5,066 shhhercommand.h
- - rwxr-xr-x 27,569 shhhseqscommand.cpp
- - rwxr-xr-x 1,729 shhhseqscommand.h
- - rwxr-xr-x 40,797 sortseqscommand.cpp
- - rwxr-xr-x 1,178 sortseqscommand.h
- - rwxr-xr-x 18,256 sparcccommand.cpp
- - rwxr-xr-x 1,945 sparcccommand.h
- - rw-r--r-- 32,572 splitabundcommand.cpp
- - rwxr-xr-x 1,914 splitabundcommand.h
- - rwxr-xr-x 43,110 splitgroupscommand.cpp
- - rwxr-xr-x 9,058 splitgroupscommand.h
- - rw-r--r-- 118,713 sracommand.cpp
- - rwxr-xr-x 3,054 sracommand.h
- - rwxr-xr-x 24,941 srainfocommand.cpp
- - rw-r--r-- 1,610 srainfocommand.hpp
- - rw-r--r-- 62,849 subsamplecommand.cpp
- - rwxr-xr-x 1,821 subsamplecommand.h
- - rwxr-xr-x 32,849 summarycommand.cpp
- - rwxr-xr-x 1,535 summarycommand.h
- - rwxr-xr-x 15,183 summaryqualcommand.cpp
- - rwxr-xr-x 1,351 summaryqualcommand.h
- - rwxr-xr-x 42,070 summarysharedcommand.cpp
- - rwxr-xr-x 4,006 summarysharedcommand.h
- - rwxr-xr-x 14,867 summarytaxcommand.cpp
- - rwxr-xr-x 1,291 summarytaxcommand.h
- - rwxr-xr-x 3,691 systemcommand.cpp
- - rwxr-xr-x 870 systemcommand.h
- - rw-r--r-- 24,783 translateseqscommand.cpp
- - rw-r--r-- 4,419 translateseqscommand.hpp
- - rwxr-xr-x 42,527 treesharedcommand.cpp
- - rwxr-xr-x 3,353 treesharedcommand.h
- - rwxr-xr-x 46,830 trimflowscommand.cpp
- - rwxr-xr-x 1,791 trimflowscommand.h
- - rw-r--r-- 64,731 trimseqscommand.cpp
- - rwxr-xr-x 2,165 trimseqscommand.h
- - rwxr-xr-x 36,924 unifracunweightedcommand.cpp
- - rwxr-xr-x 2,582 unifracunweightedcommand.h
- - rwxr-xr-x 43,564 unifracweightedcommand.cpp
- - rwxr-xr-x 2,422 unifracweightedcommand.h
- - rwxr-xr-x 21,086 uniqueseqscommand.cpp
- - rwxr-xr-x 1,389 uniqueseqscommand.h
- - rwxr-xr-x 23,907 venncommand.cpp
- - rwxr-xr-x 1,349 venncommand.h