MONKEY specifications


Unique identifier OMICS_12882
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data MONKEY takes as input a multiple sequence alignment, a tree describing the relationship of the aligned species, a model of a transcription factor's binding specificity and a model for background noncoding DNA.
Output data It returns, for each position in the alignment, a likelihood ratio comparing the probability that the position is a conserved binding site for the selected factor compared to the probability that the position is background.
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes



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  • person_outline Michael Eisen <>

Publication for MONKEY

MONKEY institution(s)
Graduate Group in Biophysics, University of California, Berkeley, CA, USA; Center for Integrative Genomics, University of California, Berkeley, CA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; Department of Genome Sciences, Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, Berkeley, CA, USA

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