TIPP:Taxonomic Identification and Phylogenetic Profiling

TitleTIPP:Taxonomic Identification and Phylogenetic Profiling
Publication TypeJournal Articles
Year of Publication2014
AuthorsNguyen N-phuong, Mirarab S, Liu B, Pop M, Warnow T
Date PublishedOctober 29, 2014
AbstractMotivation: 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 TIPP (taxon identification and phylogenetic profiling), a new marker-based taxon identification and abundance profiling method. TIPP combines SEPP, 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.Availability: Software and supplementary materials are available at http://www.cs.utexas.edu/users/phylo/software/sepp/tipp-submission/.Cont... warnow@illinois.edu