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Associated diseases

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PHYLOSCANNER specifications


Unique identifier OMICS_24367
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python, R, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.4.0
Stability Stable
Maintained Yes



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  • person_outline Chris Wymant <>

PHYLOSCANNER in publications

PMCID: 5927459
PMID: 29668677
DOI: 10.1371/journal.pcbi.1006117

[…] another similarly looking and equally concerning problem is sample contamination. we recommend sequencing data to be tested for possible contaminations and multiple infections using methods such as phyloscanner [] prior to being investigated with badtrip. in our ebola dataset we found no obvious pattern of mixed infection or contamination (like an excess of similar frequency snps in one […]

PMCID: 5625587
PMID: 28953320
DOI: 10.7448/IAS.20.6.22253

[…] hiv genomes using two commands, by mapping (aligning) reads to a reference genome constructed specifically for each sample to maximize accuracy, then finding the consensus of the reads. our program ‘phyloscanner’ interprets mapped reads with a single command. this extracts all patients’ reads in a sliding window of the genome, processes and aligns them, constructs a phylogeny with raxml, […]

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PHYLOSCANNER institution(s)
Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, UK; Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, UK; Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, UK; Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, UK; Department of Veterinary Medicine, University of Cambridge, UK; Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
PHYLOSCANNER funding source(s)
Supported by ERC Advanced Grant PBDR-339251.


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