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ghost-tree specifications

Information


Unique identifier OMICS_11553
Name ghost-tree
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data ghost-tree takes as input (1) the Foundation Alignment (for example, the Silva 18S alignment) where sequences are annotated with taxonomy; (2) the Extension Sequence Collection (for example, unaligned ITS sequences from the UNITE database); and (3) a taxonomy map, which contains taxonomic annotations of the sequences in (2).
Operating system Unix/Linux
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Stability Stable
Requirements
MUSCLE, FastTree, SUMACLUST, ghost-tree
Maintained Yes

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Documentation


Maintainer


  • person_outline Jennifer Fouquier <>

Publication for ghost-tree

ghost-tree in publication

PMCID: 5840654
PMID: 29546248
DOI: 10.1128/mSystems.00140-17

[…] were collapsed into one taxon, decreasing the number of taxa from 123 to 96 across all samples. alpha and beta diversity were calculated using qiime v.1.8.0 (), with the use of the dynamic 100 ghost-tree (0116_s) for phylogenetic metrics (). only one sample per individual, per time point, and per body site was retained for subsequent analysis, as some participants had multiple samples […]


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ghost-tree institution(s)
Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA; Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA; Institute for Systems Biology, Seattle, WA, USA; Department of Pediatrics, and Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA; Department of Biology, San Diego State University, San Diego, CA, USA; San Diego State University, San Diego, CA, USA
ghost-tree funding source(s)
This work was supported in part by grants from the Alfred P. Sloan Foundation.

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