S-LIBSHUFF statistics

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Protocols

S-LIBSHUFF specifications

Information


Unique identifier OMICS_14268
Name S-LIBSHUFF
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A distance matrix generated by the DNADIST program.
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.22
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Jo Handelsman

Publication for S-LIBSHUFF

S-LIBSHUFF citations

 (5)
call_split

Resilience of the prokaryotic microbial community of Acropora digitifera to elevated temperature

2017
PMCID: 5552946
PMID: 28425179
DOI: 10.1002/mbo3.478
call_split See protocol

[…] een samples was assessed by weighted Unifrac analysis with a p‐value cutoff of 0.05 (Lozupone & Knight, ). The similarity of community structure between control and treated samples was assessed using ʃ‐Libshuff, analysis of molecular variance (AMOVA) and homogeneity of molecular variance (HOMOVA) (Schloss, ; Singleton, Furlong, Rathbun, & Whitman, ). Libraries were considered significantly differe […]

call_split

Comparative Analysis of the Methanogen Diversity in Horse and Pony by Using mcrA Gene and Archaeal 16S rRNA Gene Clone Libraries

2014
PMCID: 3941164
PMID: 24678264
DOI: 10.1155/2014/483574
call_split See protocol

[…] 100, where N is the total number of clones and n is an OTU that consists of only 1 clone. The evenness (E) was calculated from the H′ using the following formula: E = H′/H max⁡ [], where H max⁡ = 1n(S). LIBSHUFF analysis was used to calculate the statistical significance of the differences between the 2 libraries using the mothur program []. […]

library_books

Effect of antimicrobial growth promoter administration on the intestinal microbiota of beef cattle

2013
PMCID: 3639104
PMID: 23578222
DOI: 10.1186/1757-4749-5-8

[…] ignment tool [] and putative chimeras were detected using Mallard [] and the GreenGenes chimera check []. Putative chimeras were confirmed with Pintail [], and were excluded from subsequent analyses. S-Libshuff web [] was used to ensure that there was not a significant difference between replicate libraries (P > 0.05). Replicate libraries were combined, and Mothur was used to construct rarefaction […]

library_books

Taxonomic Richness of Yeasts in Japan within Subtropical and Cool Temperate Areas

2012
PLoS One
PMCID: 3511277
PMID: 23226383
DOI: 10.1371/journal.pone.0050784

[…] i-Soil. Based on sequences of the isolates, the diversity of the yeast community was compared among these groups using four methods: parsimony-test, unweighted UniFrac-test, weighted UniFrac-test and S-LIBSHUFF analysis, and each group was significantly distinct (p<0.001) by all methods. The results statistically supported the taxonomic diversity of the tentative identification. […]

library_books

Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data

2012
PLoS One
PMCID: 3494672
PMID: 23152838
DOI: 10.1371/journal.pone.0048996

[…] arity to other communities. Several other methods exist that depend on sequence and phylogeny comparisons (e.g., AMOVA, Tree Climber) or diversity indices and community coverage (e.g., LIBSHUFF and S-LIBSHUFF ). All the above methods compare two libraries of sequences, however, because of the computational complexity of calculating phylogenetic trees and generating huge pairwise distance matrice […]

Citations

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S-LIBSHUFF institution(s)
Department of Plant Pathology, University of Wisconsin—Madison, Madison, WI, USA; Department of Botany, University of Wisconsin—Madison, Madison, WI, USA; Department of Statistics, University of Wisconsin—Madison, Madison, WI, USA
S-LIBSHUFF funding source(s)
This work was supported by a USDA postdoctoral fellowship in soil biology, an NIH grant, the NSF Microbial Observatory program (MCB- 0132085), the Howard Hughes Medical Institute, and the University of Wisconsin—Madison College of Agricultural and Life Sciences.

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