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comparison mothur/tool-data/mothur_calculators.loc.sample @ 15:a6189f58fedb

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Mothur - updated for Mothur version 1.22.0
author Jim Johnson <jj@umn.edu>
date Tue, 08 Nov 2011 11:45:32 -0600
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14:ee59e5cff3ba 15:a6189f58fedb
1 #This is a sample file distributed with Galaxy that enables
2 # Mothur tools to present a choice of values for calculators
3 # (There aren't any local files to point to, so this doesn't need to be modified)
4 # source - http://www.mothur.org/wiki/Calculators
5 #
6 #file has this format (fields are separated by TAB characters):
7 #
8 ##
9 # collect.single ace, bergerparker, boneh, bootstrap, bstick, chao, coverage, default, efron, geometric, goodscoverage, heip, invsimpson, jack, logseries, npshannon, nseqs, qstat, shannon, shannoneven, shen, simpson, simpsoneven, smithwilson, sobs, solow
10 # summary.single ace, bergerparker, boneh, bootstrap, bstick, chao, coverage, default, efron, geometric, goodscoverage, heip, invsimpson, jack, logseries, npshannon, nseqs, qstat, shannon, shannoneven, shen, simpson, simpsoneven, smithwilson, sobs, solow
11 # rarefaction.single ace, bootstrap, chao, coverage, default, heip, invsimpson, jack, npshannon, nseqs, shannon, shannoneven, simpson, simpsoneven, smithwilson, sobs
12 ##
13 # collect.shared anderberg, braycurtis, canberra, default, gower, hamming, hellinger, jabund, jclass, jest, kstest, kulczynski, kulczynskicody, lennon, manhattan, memchi2, memchord, memeuclidean, mempearson, morisitahorn, ochiai, odum, sharedace, sharedchao, sharednseqs, sharedsobs, soergel, sorabund, sorclass, sorest, spearman, speciesprofile, structchi2, structchord, structeuclidean, structkulczynski, structpearson, thetan, thetayc, whittaker
14 # summary.shared anderberg, braycurtis, canberra, default, gower, hamming, hellinger, jabund, jclass, jest, kstest, kulczynski, kulczynskicody, lennon, manhattan, memchi2, memchord, memeuclidean, mempearson, morisitahorn, ochiai, odum, sharedace, sharedchao, sharednseqs, sharedsobs, soergel, sorabund, sorclass, sorest, spearman, speciesprofile, structchi2, structchord, structeuclidean, structkulczynski, structpearson, thetan, thetayc, whittaker
15 # dist.shared anderberg, braycurtis, canberra, gower, hamming, hellinger, jabund, jclass, jest, kstest, kulczynski, kulczynskicody, lennon, manhattan, memchi2, memchord, memeuclidean, mempearson, morisitahorn, ochiai, odum, sharedace, sharedchao, sharednseqs, sharedsobs, soergel, sorabund, sorclass, sorest, spearman, speciesprofile, structchi2, structchord, structeuclidean, structkulczynski, structpearson, thetan, thetayc, whittaker
16 # tree.shared anderberg, braycurtis, canberra, gower, hamming, hellinger, jabund, jclass, jest, kstest, kulczynski, kulczynskicody, lennon, manhattan, memchi2, memchord, memeuclidean, mempearson, morisitahorn, ochiai, odum, sharedace, sharedchao, sharednseqs, sharedsobs, soergel, sorabund, sorclass, sorest, spearman, speciesprofile, structchi2, structchord, structeuclidean, structkulczynski, structpearson, thetan, thetayc, whittaker
17 # heatmap.sim braycurtis, jabund, jclass, jest, morisitahorn, sorabund, sorclass, sorest, thetan, thetayc
18 ##
19 # venn sobs,chao,ace sharedsobs,sharedchao,sharedace
20 # rarefaction.shared sharednseqs,sharedobserved
21 #
22 ##
23 #<calculator> <mult> <mult2> <category> <description>
24 #
25 ##Community richness
26 ace single sing Community richness the ACE estimator
27 bootstrap single sing Community richness the bootstrap estimator
28 chao single sing Community richness the Chao1 estimator
29 jack single sing Community richness the jackknife estimator
30 sobs single sing Community richness the observed richness
31 ##Community evenness
32 simpsoneven single sing Community evenness a Simpson index-based measure of evenness
33 shannoneven single sing Community evenness a Shannon index-based measure of evenness
34 heip single sing Community evenness Heip's metric of community evenness
35 smithwilson single sing Community evenness Smith and Wilson's metric of community evenness
36 ##Community diversity
37 bergerparker single xxxx Community diversity the Berger-Parker index
38 coverage single sing Community diversity the sampling coverage
39 goodscoverage single sing Community diversity the Good's estimate of sampling coverage
40 invsimpson single sing Community diversity the Simpson index
41 npshannon single sing Community diversity the non-parametric Shannon index
42 qstat single xxxx Community diversity the Q statistic
43 shannon single sing Community diversity the Shannon index
44 simpson single sing Community diversity the Simpson index
45 ##Estimates of number of additional OTUs observed with extra sampling
46 boneh single xxxx Estimator Boneh's estimator
47 efron single xxxx Estimator Efron's estimator
48 shen single xxxx Estimator Shen's estimator
49 solow single xxxx Estimator Solow's estimator
50 ##Statistical distributions
51 logseries single xxxx Statistical distribution tests whether observed data follow the log series distribution
52 geometric single xxxx Statistical distribution tests whether observed data follow the geometric series distribution
53 bstick single xxxx Statistical distribution tests whether observed data follow the broken stick distribution
54 ## Shared community richness
55 sharedsobs shared xxxx Shared community richness the observed richness shared between two or more samples
56 sharedchao shared xxxx Shared community richness the two or more sample shared Chao1 richness estimator
57 sharedace shared xxxx Shared community richness the two sample shared ACE richness estimator
58 ##Similarity in community membership
59 anderberg shared xxxx Community Membership Similarity the Anderberg similarity coefficient
60 jclass shared shar Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness
61 jest shared shar Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses
62 kulczynski shared xxxx Community Membership Similarity the Kulczynski similarity coefficient
63 kulczynskicody shared xxxx Community Membership Similarity the Kulczynski-Cody similarity coefficient
64 kstest shared xxxx Kolmogorov-Smirnov test
65 lennon shared xxxx Community Membership Similarity the Lennon similarity coefficient
66 ochiai shared xxxx Community Membership Similarity the Ochiai similarity coefficient
67 sorclass shared shar Community Membership Similarity the Sorenson similarity coefficient based on the observed richness
68 sorest shared shar Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses
69 whittaker shared xxxx Community Membership Similarity the Whittaker similarity coefficient
70 hamming shared xxxx Community Membership Similarity -
71 memchi2 shared xxxx Community Membership Similarity -
72 memchord shared xxxx Community Membership Similarity -
73 memeuclidean shared xxxx Community Membership Similarity -
74 mempearson shared xxxx Community Membership Similarity -
75 ##Similarity in community structure
76 braycurtis shared shar Community Structure Similarity the Bray-Curtis similarity coefficient
77 jabund shared shar Community Structure Similarity the abundance-based Jaccard similarity coefficient
78 morisitahorn shared shar Community Structure Similarity the Morisita-Horn similarity coefficient
79 sorabund shared shar Community Structure Similarity the abundance-based Sorenson similarity coefficient
80 thetan shared shar Community Structure Similarity the Smith theta similarity coefficient
81 thetayc shared shar Community Structure Similarity the Yue & Clayton theta similarity coefficient
82 canberra shared xxxx Community Structure Similarity -
83 gower shared xxxx Community Structure Similarity -
84 hellinger shared xxxx Community Structure Similarity -
85 manhattan shared xxxx Community Structure Similarity -
86 odum shared xxxx Community Structure Similarity -
87 soergel shared xxxx Community Structure Similarity -
88 spearman shared xxxx Community Structure Similarity -
89 speciesprofile shared xxxx Community Structure Similarity -
90 structchi2 shared xxxx Community Structure Similarity -
91 structchord shared xxxx Community Structure Similarity -
92 structeuclidean shared xxxx Community Structure Similarity -
93 structkulczynski shared xxxx Community Structure Similarity -
94 structpearson shared xxxx Community Structure Similarity -
95 ##Utility calculators
96 nseqs single sing Utility the number of sequences in a sample
97 sharednseqs shared rare Utility the number of sequences in two samples
98 sharedobserved shared rare Utility the number of sequences in two samples