Fast Unifrac statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Fast Unifrac
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Protocols

Fast Unifrac specifications

Information


Unique identifier OMICS_19783
Name Fast Unifrac
Interface Web user interface
Restrictions to use None
Programming languages Python
Computer skills Basic
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Additional information


Fast Unifrac is also available into the PyCogent package available at https://github.com/pycogent/pycogent/.

Publication for Fast Unifrac

Fast Unifrac citations

 (124)
call_split

Chronic fertilization of 37 years alters the phylogenetic structure of soil arbuscular mycorrhizal fungi in Chinese Mollisols

2018
PMCID: 5904092
PMID: 29667106
DOI: 10.1186/s13568-018-0587-2
call_split See protocol

[…] belonged to Glomeromycota phylum were obtained. The alpha diversity indices of AMF were calculated using Mothur (Schloss et al. ). A principal coordinate analysis (PCoA) on the basis of the weighted Fast UniFrac metric was carried out to examine the effect of inorganic and organic fertilizers on AMF community composition and to compare between-sample variations (Marsh et al. ). Redundancy analysi […]

call_split

Effect of vitamin C on azoxymethane (AOM)/dextran sulfate sodium (DSS) induced colitis associated early colon cancer in mice

2018
PMCID: 5886961
PMID: 29629026
DOI: 10.4162/nrp.2018.12.2.101
call_split See protocol

[…] as used to define species richness and diversity. In addition, the Chao 1 and Shannon estimator were used to calculate microbiota richness and diversity in Mothur and a distance matrix was created in Fast UniFrac (Chunlab Inc.: Seoul, Korea). […]

library_books

Bacteriome from Pinus arizonica and P. durangensis: Diversity, Comparison of Assemblages, and Overlapping Degree with the Gut Bacterial Community of a Bark Beetle That Kills Pines

2018
Front Microbiol
PMCID: 5797664
PMID: 29441055
DOI: 10.3389/fmicb.2018.00077

[…] usly reported for D. rhizophagus ().The β diversity of endophytic bacterial communities of each pine species was estimated using the Bray–Curtis dissimilarity index as well as unweighted and weighted Fast UniFrac distances metrics. Both UniFrac estimators are based on phylogenetic richness, but weighted UniFrac analysis also considers the relative abundance of OTUs (). This information is extracte […]

call_split

Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets

2017
Microbiome
PMCID: 5745981
PMID: 29282153
DOI: 10.1186/s40168-017-0390-3
call_split See protocol

[…] e number of sequences was considered appropriate for further analyses. The Shannon diversity index was calculated as a measure of alpha-diversity. Beta-diversity among samples was calculated using by Fast Unifrac [], and visualised using principal component analysis (PCA). Krona analysis was used to allow for a complete visual exploration of relative abundances within the complex hierarchies of mi […]

library_books

Mosquito vector‐associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod‐borne diseases

2017
Ecol Evol
PMCID: 5773340
PMID: 29375803
DOI: 10.1002/ece3.3676

[…] o assess beta‐diversity, indicative of the intersample differences between mosquito microbiota, we calculated the normalized weighted UniFrac distances (Lozupone & Knight, ) of all sample pairs using Fast UniFrac (Hamady, Lozupone, & Knight, ). The input phylogenetic trees for Fast UniFrac were constructed using FastTree (Price, Dehal, & Arkin, ) which infers approximately maximum‐likelihood tree […]

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Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform

2017
PMCID: 5697093
PMID: 29201150
DOI: 10.1186/s13099-017-0218-5
call_split See protocol

[…] nlab, Inc.). The alpha diversity analysis, including rarefaction curve and diversity indices, was carried out. The beta diversity, including principal coordinate analysis (PCA), was analyzed based on Fast UniFrac []. The core microbiota was defined as including microorganisms present in more than 80% of dog feces in each diet group, and at the same time accounting for more than 0.1% of the total m […]


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Fast Unifrac institution(s)
Department of Computer Science, University of Colorado, Boulder, CO, USA; Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA; Center for Genome Sciences, Washington University School of Medicine, St. Louis, MO, USA
Fast Unifrac funding source(s)
Supported in part by NIH grants 1R01HG004872-01, 1U01HG004866-01, and P01DK078669, by the Crohn's and Colitis Foundation of America, and by a Bill and Melinda Gates Foundation Mal-ED Network Discovery Project.

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