Tag: Phylogenetic Profiling

ProtPhylo – Prediction of Protein-to-protein and Phenotype-to-protein Functional Associations based on Phylogenetic Profiling

ProtPhylo

:: DESCRIPTION

ProtPhylo is a web server to retrieve phenotype-to-protein (Phenotype Phylogenetic Profiling) and protein-to-protein (Protein Phylogenetic Profiling) functional associations based on comparative genomics analysis of 2048 complete genomes (1678 bacteria, 255 eukaryotes and 115 archea).

::DEVELOPER

ProtPhylo team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling.
Cheng Y, Perocchi F.
Nucleic Acids Res. 2015 May 8. pii: gkv455.

TIPP – Taxon Identification and Phylogenetic Profiling

TIPP

:: DESCRIPTION

TIPP is a new 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.

::DEVELOPER

The Warnow Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TIPP

:: MORE INFORMATION

Citation

TIPP:Taxonomic Identification and Phylogenetic Profiling.
Nguyen NP, Mirarab S, Liu B, Pop M, Warnow T.
Bioinformatics. 2014 Oct 29. pii: btu721.