Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tool-data/mothur_calulators.loc @ 11:2ab2418616af draft
tool_dependencies.xml - now working, added chmod for uchime_src/mk, and changed move_file
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 30 Nov 2012 10:51:36 -0600 |
| parents | 591e72edabed |
| children |
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#This is a sample file distributed with Galaxy that enables # Mothur tools to present a choice of values for calculators # source - http://www.mothur.org/wiki/Calculators #file has this format (fields are separated by TAB characters): # # venn sobs,chao,ace sharedsobs,sharedchao,sharedace # rarefaction.shared sharednseqs,sharedobserved # rarefaction.single ace,bootstrap,chao,coverage,heip,invsimpson,jack,npshannon,nseqs,shannon,shannoneven,simpson,simpsoneven,smithwilson,sobs # dist.shared braycurtis,jabund,jclass,jest,morisitahorn,sorabund,sorclass,sorest,thetan,thetayc # tree.shared braycurtis,jabund,jclass,jest,morisitahorn,sorabund,sorclass,sorest,thetan,thetayc # heatmap.sim braycurtis,jabund,jclass,jest,morisitahorn,sorabund,sorclass,sorest,thetan,thetayc # collect.shared anderberg,braycurtis,jabund,jclass,jest,kstest,kulczynski,kulczynskicody,lennon,morisitahorn,ochiai,sharedace,sharedchao,sharednseqs,sharedsobs,sorabund,sorclass,sorest,thetan,thetayc,whittaker # summary.shared anderberg,braycurtis,jabund,jclass,jest,kstest,kulczynski,kulczynskicody,lennon,morisitahorn,ochiai,sharedace,sharedchao,sharednseqs,sharedsobs,sorabund,sorclass,sorest,thetan,thetayc,whittaker # collect.single ace,bergerparker,boneh,bootstrap,bstick,chao,coverage,efron,geometric,goodscoverage,heip,invsimpson,jack,logseries,npshannon,nseqs,qstat,shannon,shannoneven,shen,simpson,simpsoneven,smithwilson,sobs,solow # summary.single ace,bergerparker,boneh,bootstrap,bstick,chao,coverage,efron,geometric,goodscoverage,heip,invsimpson,jack,logseries,npshannon,nseqs,qstat,shannon,shannoneven,shen,simpson,simpsoneven,smithwilson,sobs,solow # #<calculator> <mult> <mult2> <category> <description> # #Community richness sobs single sing Community richness the observed richness chao single sing Community richness the Chao1 estimator ace single sing Community richness the ACE estimator jack single sing Community richness the jackknife estimator bootstrap single sing Community richness the bootstrap estimator #Community diversity bergerparker single xxxx Community diversity the Berger-Parker index shannon single sing Community diversity the Shannon index npshannon single sing Community diversity the non-parametric Shannon index simpson single sing Community diversity the Simpson index simpsoneven single sing Community diversity the Simpson index invsimpson single sing Community diversity the Simpson index coverage single sing Community diversity the sampling coverage coverage qstat single xxxx Community diversity the Q statistic #Estimates of number of additional OTUs observed with extra sampling boneh single xxxx Estimator Boneh's estimator efron single xxxx Estimator Efron's estimator shen single xxxx Estimator Shen's estimator solow single xxxx Estimator Solow's estimator #Statistical distributions logseries single xxxx Statistical distribution tests whether observed data follow the log series distribution geometric single xxxx Statistical distribution tests whether observed data follow the geometric series distribution bstick single xxxx Statistical distribution tests whether observed data follow the broken stick distribution # Shared community richness sharedsobs shared xxxx Shared community richness the observed richness shared between two or more samples sharedchao shared xxxx Shared community richness the two or more sample shared Chao1 richness estimator sharedace shared xxxx Shared community richness the two sample shared ACE richness estimator #Similarity in community membership anderberg shared xxxx Community Membership Similarity the Anderberg similarity coefficient jclass shared shar Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness jest shared shar Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses kulczynski shared xxxx Community Membership Similarity the Kulczynski similarity coefficient kulczynskicody shared xxxx Community Membership Similarity the Kulczynski-Cody similarity coefficient lennon shared xxxx Community Membership Similarity the Lennon similarity coefficient ochiai shared xxxx Community Membership Similarity the Ochiai similarity coefficient sorclass shared shar Community Membership Similarity the Sorenson similarity coefficient based on the observed richness sorest shared shar Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses whittaker shared xxxx Community Membership Similarity the Whittaker similarity coefficient #Similarity in community structure braycurtis shared shar Community Structure Similarity the Bray-Curtis similarity coefficient jabund shared shar Community Structure Similarity the abundance-based Jaccard similarity coefficient morisitahorn shared shar Community Structure Similarity the Morisita-Horn similarity coefficient sorabund shared shar Community Structure Similarity the abundance-based Sorenson similarity coefficient thetan shared shar Community Structure Similarity the Smith theta similarity coefficient thetayc shared shar Community Structure Similarity the Yue & Clayton theta similarity coefficient #Utility calculators nseqs single sing Utility the number of sequences in a sample sharednseqs shared rare Utility the number of sequences in two samples sharedobserved shared rare Utility the number of sequences in two samples