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HipMCL specifications


Unique identifier OMICS_25848
Name HipMCL
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Aydin Buluc
  • person_outline Ariful Azad

Additional information


Publication for HipMCL

HipMCL citation


HipMCL: a high performance parallel implementation of the Markov clustering algorithm for large scale networks

Nucleic Acids Res
PMCID: 5888241
PMID: 29315405
DOI: 10.1093/nar/gkx1313

[…] In order to construct several networks to test the behaviour of HipMCL, we collected all viral, eukaryotic and archaeal proteins from the isolate genomes hosted by the IMG platform and created three domain-specific non-redundant datasets at 100% sequence similarit […]

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HipMCL institution(s)
Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, USA; Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
HipMCL funding source(s)
Supported by US Department of Energy (DOE) Joint Genome Institute [DE-AC02–05CH11231, in part], a DOE Office of Science User Facility; Applied Mathematics program of the DOE Office of Advanced Scientific Computing Research [DEAC02–05CH11231, in part], Office of Science of the US Department of Energy; Exascale Computing Project (17- SC-20-SC), a collaborative effort of the U.S. Department of Energy Office of Science and the National Nuclear Security Administration.

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