Mercurial > repos > jjohnson > mothur_toolsuite
diff mothur/tool-data/mothur_calulators.loc @ 0:591e72edabed
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
| author | jjohnson |
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| date | Tue, 07 Jun 2011 16:54:12 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tool-data/mothur_calulators.loc Tue Jun 07 16:54:12 2011 -0400 @@ -0,0 +1,68 @@ +#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