Nguyen, Nam, Siavash Mirarab, Bo Liu, Mihai Pop, and Tandy Warnow. “TIPP: Taxonomic Identification and Phylogenetic Profiling.” Bioinformatics 30, no. 24 (2014): 3548–55. doi:10.1093/bioinformatics/btu721.
TIPP (Taxon Identification and Phylogenetic Profiling) is a marker-based method developed for abundance profiling of metagenomic data. TIPP uses a collection of 30 universal marker genes and bins the fragments to the marker genes. For each set of fragments binned to a marker gene, TIPP classifies the fragments by inserting the fragments into the taxonomic tree estimated on the marker gene. TIPP performs classification in a phylogenetic framework, and thus relies on a reference alignment and tree on full length sequences of known organisms belonging to the same gene, from which fragments are being classified.
The default usage of TIPP operates as follows:
For each fragment in X, TIPP uses SEPP (Mirarab et al. 2012), a method for phylogenetic placement, to insert the fragment into the taxonomy T*. However, whereas SEPP generated only the single best alignment for each query sequence, and used the best alignment to inser the query sequence into the tree, TIPP can potentially generate many alignments (each with statistical support scores) and many placements. TIPP then uses the placements to assign support to the nodes in the taxonomy and accepts the classification of a fragment if it has sufficient statistical support (default setting is 95%). TIPP allows the user to modify the required statistical support values, the alignment subset size. See the README file for more information.
TIPP is available for download and installation on Linux and Mac machines, but note that almost all testing has been done on Linux.
Installation and tutorial: After downloading the zip files, uncompress the zip files to your favorite location.
TIPP is under active research development, both by the Warnow Lab (now at UIUC) and also by her former PhD students Siavash Mirarab and Nam Nguyen (both at UCSD). We welcome research collaborations. Please contact any of us by email.