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annotate mothur/tool-data/mothur_calculators.loc @ 10:51a065071567 draft

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Need to "cd Mothur.soure && make" in tool_dependencies.xml
author Jim Johnson <jj@umn.edu>
date Fri, 30 Nov 2012 09:53:52 -0600
parents e076d95dbdb5
children
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1 #This is a sample file distributed with Galaxy that enables
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2 # Mothur tools to present a choice of values for calculators
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3 # source - http://www.mothur.org/wiki/Calculators
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4 #file has this format (fields are separated by TAB characters):
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5 #
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6 ##
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7 # 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
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8 # 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
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9 # rarefaction.single ace, bootstrap, chao, coverage, default, heip, invsimpson, jack, npshannon, nseqs, shannon, shannoneven, simpson, simpsoneven, smithwilson, sobs
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10 ##
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11 # 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
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12 # 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
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13 # 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
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14 # 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
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15 # heatmap.sim braycurtis, jabund, jclass, jest, morisitahorn, sorabund, sorclass, sorest, thetan, thetayc
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16 ##
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17 # venn sobs,chao,ace sharedsobs,sharedchao,sharedace
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18 # rarefaction.shared sharednseqs,sharedobserved
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19 #
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20 ##
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21 #<calculator> <mult> <mult2> <category> <description>
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22 #
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23 ##Community richness
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24 ace single sing Community richness the ACE estimator
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25 bootstrap single sing Community richness the bootstrap estimator
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26 chao single sing Community richness the Chao1 estimator
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27 jack single sing Community richness the jackknife estimator
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28 sobs single sing Community richness the observed richness
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29 ##Community evenness
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30 simpsoneven single sing Community evenness a Simpson index-based measure of evenness
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31 shannoneven single sing Community evenness a Shannon index-based measure of evenness
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32 heip single sing Community evenness Heip's metric of community evenness
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33 smithwilson single sing Community evenness Smith and Wilson's metric of community evenness
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34 ##Community diversity
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35 bergerparker single xxxx Community diversity the Berger-Parker index
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36 coverage single sing Community diversity the sampling coverage
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37 goodscoverage single sing Community diversity the Good's estimate of sampling coverage
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38 invsimpson single sing Community diversity the Simpson index
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39 npshannon single sing Community diversity the non-parametric Shannon index
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40 qstat single xxxx Community diversity the Q statistic
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41 shannon single sing Community diversity the Shannon index
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42 simpson single sing Community diversity the Simpson index
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43 ##Estimates of number of additional OTUs observed with extra sampling
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44 boneh single xxxx Estimator Boneh's estimator
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45 efron single xxxx Estimator Efron's estimator
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46 shen single xxxx Estimator Shen's estimator
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47 solow single xxxx Estimator Solow's estimator
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48 ##Statistical distributions
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49 logseries single xxxx Statistical distribution tests whether observed data follow the log series distribution
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50 geometric single xxxx Statistical distribution tests whether observed data follow the geometric series distribution
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51 bstick single xxxx Statistical distribution tests whether observed data follow the broken stick distribution
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52 ## Shared community richness
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53 sharedsobs shared xxxx Shared community richness the observed richness shared between two or more samples
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54 sharedchao shared xxxx Shared community richness the two or more sample shared Chao1 richness estimator
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55 sharedace shared xxxx Shared community richness the two sample shared ACE richness estimator
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56 ##Similarity in community membership
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57 anderberg shared xxxx Community Membership Similarity the Anderberg similarity coefficient
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58 jclass shared shar Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness
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59 jest shared shar Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses
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60 kulczynski shared xxxx Community Membership Similarity the Kulczynski similarity coefficient
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61 kulczynskicody shared xxxx Community Membership Similarity the Kulczynski-Cody similarity coefficient
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62 kstest shared xxxx Kolmogorov-Smirnov test
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63 lennon shared xxxx Community Membership Similarity the Lennon similarity coefficient
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64 ochiai shared xxxx Community Membership Similarity the Ochiai similarity coefficient
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65 sorclass shared shar Community Membership Similarity the Sorenson similarity coefficient based on the observed richness
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66 sorest shared shar Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses
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67 whittaker shared xxxx Community Membership Similarity the Whittaker similarity coefficient
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68 hamming shared xxxx Community Membership Similarity -
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69 memchi2 shared xxxx Community Membership Similarity -
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70 memchord shared xxxx Community Membership Similarity -
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71 memeuclidean shared xxxx Community Membership Similarity -
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72 mempearson shared xxxx Community Membership Similarity -
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73 ##Similarity in community structure
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74 braycurtis shared shar Community Structure Similarity the Bray-Curtis similarity coefficient
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75 jabund shared shar Community Structure Similarity the abundance-based Jaccard similarity coefficient
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76 morisitahorn shared shar Community Structure Similarity the Morisita-Horn similarity coefficient
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77 sorabund shared shar Community Structure Similarity the abundance-based Sorenson similarity coefficient
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78 thetan shared shar Community Structure Similarity the Smith theta similarity coefficient
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79 thetayc shared shar Community Structure Similarity the Yue & Clayton theta similarity coefficient
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80 canberra shared xxxx Community Structure Similarity -
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81 gower shared xxxx Community Structure Similarity -
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82 hellinger shared xxxx Community Structure Similarity -
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83 manhattan shared xxxx Community Structure Similarity -
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84 odum shared xxxx Community Structure Similarity -
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85 soergel shared xxxx Community Structure Similarity -
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86 spearman shared xxxx Community Structure Similarity -
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87 speciesprofile shared xxxx Community Structure Similarity -
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88 structchi2 shared xxxx Community Structure Similarity -
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89 structchord shared xxxx Community Structure Similarity -
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90 structeuclidean shared xxxx Community Structure Similarity -
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91 structkulczynski shared xxxx Community Structure Similarity -
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92 structpearson shared xxxx Community Structure Similarity -
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93 ##Utility calculators
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94 nseqs single sing Utility the number of sequences in a sample
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95 sharednseqs shared rare Utility the number of sequences in two samples
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96 sharedobserved shared rare Utility the number of sequences in two samples