TIPP: taxonomic identification and phylogenetic profiling

Nam-Phuong Nguyen; Siavash Mirarab; Bo Liu; Mihai Pop; Tandy Warnow

doi:10.1093/bioinformatics/btu721

TIPP: taxonomic identification and phylogenetic profiling

Bioinformatics. 2014 Dec 15;30(24):3548-55. doi: 10.1093/bioinformatics/btu721. Epub 2014 Oct 29.

Authors

Nam-Phuong Nguyen¹, Siavash Mirarab¹, Bo Liu¹, Mihai Pop¹, Tandy Warnow²

Affiliations

¹ Department of Computer Science, The University of Texas at Austin, Austin, TX USA, Center for Bioinformatics and Computational Biology, University of Maryland at College Park, College Park, MD USA, Department of Bioengineering, The University of Illinois at Urbana-Champaign, Urbana, IL USA and Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL USA.
² Department of Computer Science, The University of Texas at Austin, Austin, TX USA, Center for Bioinformatics and Computational Biology, University of Maryland at College Park, College Park, MD USA, Department of Bioengineering, The University of Illinois at Urbana-Champaign, Urbana, IL USA and Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL USA Department of Computer Science, The University of Texas at Austin, Austin, TX USA, Center for Bioinformatics and Computational Biology, University of Maryland at College Park, College Park, MD USA, Department of Bioengineering, The University of Illinois at Urbana-Champaign, Urbana, IL USA and Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL USA Department of Computer Science, The University of Texas at Austin, Austin, TX USA, Center for Bioinformatics and Computational Biology, University of Maryland at College Park, College Park, MD USA, Department of Bioengineering, The University of Illinois at Urbana-Champaign, Urbana, IL USA and Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL USA.

Abstract

Motivation: Abundance profiling (also called 'phylogenetic profiling') is a crucial step in understanding the diversity of a metagenomic sample, and one of the basic techniques used for this is taxonomic identification of the metagenomic reads.

Results: We present taxon identification and phylogenetic profiling (TIPP), a new marker-based taxon identification and abundance profiling method. TIPP combines SAT\'e-enabled phylogenetic placement a phylogenetic placement method, with statistical techniques to control the classification precision and recall, and results in improved abundance profiles. TIPP is highly accurate even in the presence of high indel errors and novel genomes, and matches or improves on previous approaches, including NBC, mOTU, PhymmBL, MetaPhyler and MetaPhlAn.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Algorithms
INDEL Mutation
Metagenomics / methods*
Phylogeny*
Sequence Alignment

Abstract

Publication types

MeSH terms

Grants and funding