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AlignMCL specifications


Unique identifier OMICS_14920
Name AlignMCL
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Protein interaction networks, homology relationships.
Output data The interspecies and infraspecies analysis results, the ranked functional modules.
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.2
Stability Stable
Maintained Yes


No version available



  • person_outline Marco Mina

Publication for AlignMCL

AlignMCL citations


Unified Alignment of Protein Protein Interaction Networks

Sci Rep
PMCID: 5430463
PMID: 28424527
DOI: 10.1038/s41598-017-01085-9

[…] pings. However, local aligners focus on the most conserved regions of the networks, and thus return very small alignments. Although local aligners are not designed to align large networks (AlignNemo, AlignMCL and LocalAli all encounter memory issues on our datasets), we were able to use AlignNemo to align our smallest pair of networks, R. norvegicus PPI network (1,657 nodes and 2,330 edges) and S. […]


Detecting conserved protein complexes using a dividing and matching algorithm and unequally lenient criteria for network comparison

PMCID: 4487215
PMID: 26136815
DOI: 10.1186/s13015-015-0053-5

[…] oth match known protein complexes well and have similar functions if it takes effective strategies to partition PPI networks, for example using known protein complexes or Coach to partition. (2) UEDAMAlignMCL outperforming AlignMCL and UEDAMAlignCFinder outperforming AlignNemo confirm the effectiveness of dividing-and-matching strategy of our UEDAMAlign method. (3) The experimental results when se […]


The post genomic era of biological network alignment

EURASIP J Bioinform Syst Biol
PMCID: 5270500
PMID: 28194172
DOI: 10.1186/s13637-015-0022-9

[…] is used on the alignment graph to find relatively dense groups of nodes (i.e., proteins that have more interactions among themselves than with the rest of the network), which are AlignNemo’s output. AlignMCL [] is another recent pairwise local aligner that is robust to the choice of networks to be aligned. It is based on Markov clustering (MCL), a known graph clustering algorithm that simulates r […]


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AlignMCL institution(s)
MPBA, Fondazione Bruno Kessler (FBK), Trento, Italy; Department of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, Italy

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