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Dr. Christoph Mayer
Animal Ecology, Evolution and Biodiversity, Faculty of Biological Sciences and Biotechnology
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Animal Ecology, Evolution and Biodiversity » Members » Dr. Christoph Mayer » Software
pix pix Software written by Christoph Mayer

    Phobos - a tandem repeat search tool for genomic and other data. Most recent version: 3.3.12. The Geneious plugin needs version 3.3.10 or higher.
    Phobos is available for Windows, MacOS (Intel processors or M1 processor with Rosetta 2 installed) and Linux.
    Lately, I have only updated the command line versions needed e.g. by the Geneious software. The command line versions can also be used independently or incorporated in other pipelines.
    Commercial licences are available upon request.

    If you are interested in the Phobos software, please write an email to Christoph Mayer.


    Phobos is a highly accurate and fast search tool for
    - DNA-microsatellites,
    - DNA-minisatellites and
    - DNA-satellites

    Four of our highly cited papers for which the Phobos software has been used are:
    • Leese, F, Mayer, C, and Held, C (2008): Isolation of microsatellites from unknown genomes using known genomes as enrichment templates.
      Limnology and Oceanography: Methods 7, 412-426. doi.org/10.4319/lom.2008.6.412
    • Mayer C, Leese F, Tollrian R (2010): Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach. BMC Genomics (Abstract, PDF).
    • Read, B.A. et al. 2013. Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 499, 209-213. doi:10.1038/nature12221
    • Mock, T. et al. 2017. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature 541, 536-540. doi:10.1038/nature20803

    Is Phobos still maintained and supported? Yes!
    The last major version appeared in September 2010. There have been no bug reports for a long long time, which is good news for all users. I still intend to improve the main algorithm to make it even faster. But my time is limited and it won't be in the very near future. For 99.9% of the users speed is no problem anyway. If you have problems or if, unexpectedly, you discover a bug, please contact me!
    Changes since 2010 have mainly been adaptions to new operating systems. Please contact me if Phobos is not running on your system.

    Phobos is a multi-platform program (Mac, Linux, Windows) that comes in two versions:
    - easily scriptable CL (command-line) program. This version is used together with Geneious.
    - user friendly stand alone GUI (graphical user interface) program.
    Visualisation of tandem repeats and user friendly primer design
    Phobos has been integrated into the following molecular biology analysis tools, which in particular offer a convenient interfaces for designing flanking primers of microsatellites.
    Commercial users need to obtain a user license for Phobos directly from the author Christoph Mayer.

    • STAMP: Microsatellite marker design extension for the Staden package
      Reference:
      Kraemer, L., Beszteri, B., Gaebler-Schwarz, S., Held, C., Leese, F., Mayer, C., Poehlmann, K. & Frickenhaus, S. (2009)
      STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
      BMC Bioinformatics 10:41.

    • Phobos plugin for Geneious.
      Geneious is a commercial and easy to use DNA and protein sequence analysis tool.
      In order to use the tandem repeat detection capabilities of Phobos in Geneious one has to install the command-line version of Phobos (version 3.3.10 or higher) as well as the Phobos plugin.

    Phobos has the following main features:
    • it uses an exact, in particular non-probabilistic search algorithm,
    • it can search for perfect satellites with a pattern size of 1 - 10000 bp in complete genomes,
    • it can search for imperfect satellites in complete genomes in the pattern size range 1 - 50 bp with a high detection and alignment quality, and for patterns with a size of 10000 bp with a reduced detection and alignment quality.
    • it uses the alignment score as an optimality criterion to decide whether to extend a satellite up or downstream,
    • it detects and reports overlapping satellites,
    • it tries to extend satellites up and down stream to obtain highly accurate results which are mostly independent of the search direction,
    • it is able to find alternative alignments with different units for the same satellite,
    • it can report repeats in a variety of different output formats, including formats that show flanking regions or the alignment of the repeat region with the repeat pattern.

    When developing a DNA-satellite search tool, two main problems occur:
    The program should
    (1) detect imperfect repeats, i.e. repeats with mismatches and indels,
    (2) be able to cope with repeats that can be aligned with several different unit patterns.

    Whereas most programs focus on problem (1), problem (2) has - to my knowledge - only been solved in the
    Tandem Repeat Finder, which however uses a probabilistic, i.e. non-exact search algorithm.
    Phobos has been designed to solve problems (1) and (2).


    Development status:
    The current version of Phobos has been stable for several years now.

    Currently, I am working on the following improvements:
    - more options for reporting alternative alignments
    - detection of compound satellites


    Phobos is in use since the end of 2006:
    - it has been used to detect tandem repeats in several genome projects now.


    How to cite Phobos:
    Mayer, Christoph, Phobos 3.3.12, 2006-2010,
    <http://www.rub.de/ecoevo/cm/cm_phobos.htm>.

    If you are using the STAMP-module of the Staden-package, please also cite:
    Kraemer, L., Beszteri, B., Gaebler-Schwarz, S., Held, C., Leese, F., Mayer, C., Poehlmann, K. & Frickenhaus, S. (2009)
    STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
    BMC Bioinformatics 10:41.


    License:
    This program Phobos is copyright protected. Please send me an email, if you are interested in the Phobos software. See above.
    For academic and non-commercial usage this program can be used free of charge. Results obtained
    with this program can be published without restrictions, provided the program and its author are acknowledged by name.
    A commercial license for Phobos can be obtained from the author.


    Acknowledgements:
    I would like to thank the following colleagues for helpful conversations and support:
    Florian Leese, Universitšt Duisburg-Essen
    Christoph Held, AWI Bremerhaven
    Bank Beszteri, Universitšt Duisburg-Essen
    Stephan Frickenhaus, AWI Bremerhaven



 
 
  Last update: July 2021, Christoph Mayer