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Balík: tipp (1.0+dfsg-2)

tool for Taxonomic Identification and Phylogenetic Profiling

TIPP is a modification of SEPP for classifying query sequences (i.e. reads) using phylogenetic placement.

TIPP inserts each read into a taxonomic tree and uses the insertion location to identify the taxonomic lineage of the read. The novel idea behind TIPP is that rather than using the single best alignment and placement for taxonomic identification, it uses a collection of alignments and placements and considers statistical support for each alignment and placement.

TIPP can also be used for abundance estimation by computing an abundance profile on the reads binned to marker genes in a reference dataset.

Ostatné balíky súvisiace s balíkom tipp

  • závisí
  • odporúča
  • navrhuje
  • dep: default-jre
    Standard Java or Java compatible Runtime
  • dep: libgoogle-gson-java
    Converts Java objects into their JSON representation
  • dep: libjenkins-json-java
    Library for transforming Java objects between XML and JSON
  • dep: libjson-java
    library for transforming Java objects and XML to JSON and back again
  • dep: ncbi-blast+
    next generation suite of BLAST sequence search tools
  • dep: python3
    interactive high-level object-oriented language (default python3 version)
  • dep: python3-dendropy
    DendroPy Phylogenetic Computing Library (Python 3)
  • dep: sepp (>= 4.5.1+really4.5.1+dfsg-1~)
    phylogeny with ensembles of Hidden Markov Models

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