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AlignNemo specifications


Unique identifier OMICS_06991
Name AlignNemo
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


Publication for AlignNemo

AlignNemo citations


Unified Alignment of Protein Protein Interaction Networks

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

[…] to-many mappings. 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 ed […]


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
call_split See protocol

[…] in pair in a single network is unequal with respect to the difference of input PPI networks, which is determined by inputting parameters l and r. For example, when taking the same lenient criteria as AlignNemo and DAMAlign do, UEDAMAlign absorbs a pair of homologous proteins into its predicted conserved protein complexes if at least one of protein in the homologous protein pair connects to the pro […]


The post genomic era of biological network alignment

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

[…] t is based on Markov clustering (MCL), a known graph clustering algorithm that simulates random walks using Markov chains iteratively. AlignMCL first builds a weighted alignment graph the same way as AlignNemo. Next, it applies MCL to this graph to identify conserved protein modules. Graemlin 1.0 [] is an early multiple aligner. Based on a phylogenetic tree of species whose networks are being alig […]


Joint clustering of protein interaction networks through Markov random walk

BMC Syst Biol
PMCID: 4080334
PMID: 24565376
DOI: 10.1186/1752-0509-8-S1-S9

[…] For the SceDIP and SceBGS networks, we report the performance of ASModel, NCut, MCL, RMCL, and AlignNemo on complex prediction in terms of the number of matched reference complexes and F-measure. The detailed information such as the number of clusters (cluster size ≥ 2) and the coverage is list […]

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AlignNemo institution(s)
Department of Information Engineering, University of Padova, Padova, Italy

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