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- Software type:
- Restrictions to use:
- Operating system:
- Computer skills:
- MUSCLE, FastTree, SUMACLUST, ghost-tree (recommended)
- Command line interface
- 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).
- BSD 3-clause “New” or “Revised” License
- Issue URL:
- Jennifer Fouquier <jennietf at gmail.com>
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- (Fouquier J et al., 2016) Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses. Microbiome. PMID: 26905735 DOI: 10.1186/s40168-016-0153-6
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
This work was supported in part by grants from the Alfred P. Sloan Foundation.