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UniFrac specifications

Information


Unique identifier OMICS_14388
Name UniFrac
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++, Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 0.9.3
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Rob Knight

Publications for UniFrac

UniFrac citations

 (1599)
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Structural Alteration of Gut Microbiota during the Amelioration of Human Type 2 Diabetes with Hyperlipidemia by Metformin and a Traditional Chinese Herbal Formula: a Multicenter, Randomized, Open Label Clinical Trial

2018
MBio
PMCID: 5964358
DOI: 10.1128/mBio.02392-17
call_split See protocol

[…] normalized and log10-transformed OTU abundance table was used for the β-diversity analysis, including principal-component analysis (PCA) and principal-coordinate analysis (PCoA) based on Bray-Curtis, UniFrac, and Jaccard distances. The taxonomy of each OTU was assigned online by RDP Classifier (RDP Naive Bayesian rRNA Classifier version 2.10) with a bootstrap cutoff of 80%. […]

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Food Starch Structure Impacts Gut Microbiome Composition

2018
PMCID: 5956147
PMID: 29769378
DOI: 10.1128/mSphere.00086-18
call_split See protocol

[…] sion 13.8 (). The generated biome table was normalized using an equal subsampling size of 2,938 sequences. Distances between bacterial communities in different samples were calculated by the weighted UniFrac distance metric () in QIIME. Calypso () version 5.2 was used to generate hierarchical clustering, principal-coordinate analysis (PCoA) plots, and microbial network maps. Metagenomic function w […]

library_books

American Gut: an Open Platform for Citizen Science Microbiome Research

2018
mSystems
PMCID: 5954204
DOI: 10.1128/mSystems.00031-18

[…] plicitly. Rarefaction was used to mitigate uneven sequencing depth in accordance with the benchmarking in reference . Diversity calculations were computed using scikit-bio 0.5.1 with the exception of UniFrac (), which was computed using an unpublished algorithmic variant, Striped UniFrac (https://github.com/biocore/unifrac), which scales to larger data sets and produces results identical to previo […]

library_books

High species diversity of trichostrongyle parasite communities within and between Western Canadian commercial and conservation bison herds revealed by nemabiome metabarcoding

2018
PMCID: 5952520
PMID: 29764472
DOI: 10.1186/s13071-018-2880-y

[…] Beta diversity, at the population level, among provinces and conservation herds was assessed with the weighted UniFrac function in Mothur, which revealed marked differences in the species present between populations (where a score of 0 indicates that populations are identical and a score of 1 indicates they ar […]

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What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs

2018
PMCID: 5956146
PMID: 29743201
DOI: 10.1128/mSphere.00122-18
call_split See protocol

[…] on analysis, observed OTUs, Shannon diversity, Chao1 diversity estimation, and coverage were calculated. Two-dimensional (2D) PCoA plots based on jackknifed β diversity were calculated using weighted UniFrac indices and multiple resampling (1,000 sequences ×100 times) (). Statistical analyses were done using an Adonis test with 999 permutations. A DNA distance maximum likelihood phylogenetic tree […]

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Dynamics of phosphorus and bacterial phoX genes during the decomposition of Microcystis blooms in a mesocosm

2018
PLoS One
PMCID: 5933731
PMID: 29723219
DOI: 10.1371/journal.pone.0195205
call_split See protocol

[…] s of the phylogenetic tree was computed by 500-fold random sampling.Distance analysis was conducted for the PhoX phylogenetic tree constructed with the maximum likelihood method using online software UniFrac (http://unifrac.colorado.edu/) within each clone library []. The environmental distance matrix method was applied to perform normalised weighted analysis to obtain the UniFrac distance matrix […]

Citations

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UniFrac institution(s)
Department of Pediatrics, University of California, San Diego, CA, USA; Mathematics Department, Oregon State University, Corvallis, OR, USA; Department of Computer Science and Engineering, University of California, San Diego, CA, USA; Center for Microbiome Innovation, University of California, San Diego, CA, USA; Department of Bioengineering, University of California, San Diego, CA, USA; Biota Technology Inc., La Jolla, CA, USA
UniFrac funding source(s)
Supported by the NSF (grant DBI-1565100; award 1664803), the Alfred P. Sloan Foundation (G-2017- 9838; G-2015-13933), ONR (grant N00014-15-1-2809), and NIH–NIDDK (grant P01DK078669).

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