Introduction

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.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.

Publications

  1. TIPP: taxonomic identification and phylogenetic profiling.
    Cite this
    Nguyen NP, Mirarab S, Liu B, Pop M, Warnow T, 2014-12-01 - Bioinformatics (Oxford, England)

Credits

  1. Nam-Phuong Nguyen
    Developer

    Department of Computer Science, The University of Texas at Austin, United States of America

  2. Siavash Mirarab
    Developer

    Department of Computer Science, The University of Texas at Austin, United States of America

  3. Bo Liu
    Developer

    Department of Computer Science, The University of Texas at Austin, United States of America

  4. Mihai Pop
    Developer

    Department of Computer Science, The University of Texas at Austin, United States of America

  5. Tandy Warnow
    Investigator

    Department of Computer Science, The University of Texas at Austin, United States of America

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT006580
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByTandy Warnow