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Interpolated Variable Order Motifs to identify horizontally acquired DNA

Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the localization of the boundaries of the predicted regions. The predictions (embl format) can be automatically loaded into Artemis genome viewer freely available at:

The manuscript describing the alien_hunter algorithm is available from Bioinformatics: Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Vernikos GS, Parkhill J Bioinformatics. 2006;. PMID: 16837528

Package version:1.7-1


ALIEN_HUNTER(1)             User Commands            ALIEN_HUNTER(1)

       alien_hunter - Interpolated Variable Order Motifs for identi‐
       fication of horizontally acquired DNA

       alien_hunter <sequence.file> <output.file> [Options]

       Alien_hunter is an application for the prediction of putative
       Horizontal Gene Transfer (HGT) events with the


alien-hunter (1.7-1) unstable; urgency=low

  * Initial release (Closes: #550954)

 -- Andreas Tille <>  Wed, 14 Oct 2009 11:41:51 +0200


Name      : Alien_hunter
Contact   : George Vernikos <>
Source    :

Copyright : © 2006-2008 George Vernikos
 This program is free software; you can redistribute it and/or
 modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (

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