TIPP specifications

Information


Unique identifier OMICS_12989
Name TIPP
Alternative name Taxon Identification and Phylogenetic Profiling
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A query sequence `q` or a set of query sequences `Q`
Output data The taxonomic lineage of `q` or an abundance profile estimated on `Q`
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements
Java, Blast
Maintained No

Versioning


No version available

Documentation


Maintainer


This tool is not available anymore.

Publication for Taxon Identification and Phylogenetic Profiling

TIPP citation

library_books

Outlier detection in BLAST hits

2018
PMCID: 5863388
PMID: 29588650
DOI: 10.1186/s13015-018-0126-3

[…] ection method in a realistic setting, we tested it on a real metagenomic dataset. Since we do not know the true taxonomic label for all query sequences, we compared our results with those produced by TIPP [], a phylogenetic-tree based taxonomic assignment method. We used the RDP 2014 16S reference database for both methods []. In this dataset, there were 58,108 query sequences for which our method […]

TIPP institution(s)
Department of Computer Science, University of Texas, Austin, TX, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Department of Bioengineering, The University of Illinois, Urbana, IL, USA; Department of Computer Science, University of Illinois, Urbana, IL, USA
TIPP funding source(s)
Guggenheim Foundation Fellowship; National Science Foundation, grants DBI-1062335, DBI-1461364 and DEB 0733029; HHMI International Predoctoral Fellowship; iPlant Collaborative U.S. National Science Foundation, grant DBI-1265383; National Institutes of Health grant, R01-AI-100947; US National Science Foundation, IR/D program.

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