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PhyloPythia | Phylogenetic classification of variable-length DNA fragments

Phylogenetically classifies variable-length DNA sequence fragments. PhyloPythia is a method that uses sequence composition to phylogenetically characterize sequence fragments. The software allows the phylogenetic classification of genomic fragments ≥ 1–3 kb for all taxonomic ranks considered (domain, phylum, class, order and genus). PhyloPythia can also achieve this for fragments originating from new organisms. It was used PhyloPythia to analyse three metagenomes: the Sargasso Sea sample and two samples of Enhanced Biological Phosphorus Removal (EBPR)-sludge used in industrial wastewater processing.

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PhyloPythia classification

PhyloPythia specifications

Unique identifier:
OMICS_01459
Restrictions to use:
None
Computer skills:
Basic
Maintained:
Yes
Interface:
Web user interface
Input data:
A multiclass support vector machine (SVM) classifier with the oligonucleotide composition of variable-length genome fragments.

PhyloPythia support

Maintainer

This tool is not available anymore.

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Publications

Institution(s)

Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, NY, USA; US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA

Funding source(s)

Supported by the US Department of Energy’s Office of Science, Biological and Environmental Research Program, the University of California, Lawrence Livermore National Laboratory, under contract W-7405-Eng-48; Lawrence Berkeley National Laboratory under contract DE-AC03-76SF00098, and Los Alamos National Laboratory under contract W-7405-ENG-36.

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