PhylOligo specifications


Unique identifier OMICS_19289
Name PhylOligo
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data A multifasta of the genome assembly.
Input format FASTA
Operating system Unix/Linux, Mac OS
Programming languages Python, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.9
Stability Stable
gplots, biopython, python, samtools, numpy, matplotlib, sklearn, cython, h5py, joblib, emboss, phyloligo
Registration required No
Maintained Yes




No version available


  • person_outline Ludovic Mallet

Publication for PhylOligo

PhylOligo citation


PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies

PMCID: 5860033
PMID: 28637232
DOI: 10.1093/bioinformatics/btx396

[…] samples to automatically cluster contigs into genomes or Kraken () that relies on exact alignment of k-mers to a k-mer reference database to assign taxonomic labels to metagenomic DNA.Here we present PhylOligo, a toolset designed to explore, segment and subtract untargeted material from assembled sequences using an ab initio alignment-free approach relying only on the intrinsic oligonucleotide sig […]

PhylOligo institution(s)
INRA UR875, Unité Mathématiques et Informatique Appliquées de Toulouse (MIAT), Castanet-Tolosan, France; CNRS UMR7590, Sorbonne Universités, Université Pierre et Marie Curie, Paris 6 – MNHN – IRD – IUC, Paris, France

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