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FreClu specifications


Unique identifier OMICS_01048
Name FreClu
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



  • person_outline Shinichi Morishita

Publication for FreClu

FreClu citations


Identification of functional cis regulatory elements by sequential enrichment from a randomized synthetic DNA library

BMC Plant Biol
PMCID: 3923269
PMID: 24138055
DOI: 10.1186/1471-2229-13-164

[…] 3%; Samples 4–8, Table ). This reduction in complexity is consistent with enrichment for selective SynEs during ChIP.To further reduce complexity, we performed a clustering analysis using the program FreClu []. This analysis revealed that the library samples consisted of a large number of individual sequences, which could not be clustered. In contrast, the ChIP samples showed clustering above 40% […]


MicroRNA mediated gene regulation plays a minor role in the transcriptomic plasticity of cold acclimated Zebrafish brain tissue

BMC Genomics
PMCID: 3258298
PMID: 22168751
DOI: 10.1186/1471-2164-12-605

[…] cloning and sequencing methods.Solexa sequencing are known for its short reads, and errors can be pervasive in short-read sequencing []. To address this concern, we clustered the raw reads using the FreClu software [], which takes the read count into consideration. The results showed that this clustering process can improve the accuracy of short reads mapping (Table ). However, it did not improve […]

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FreClu institution(s)
Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan; Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Bioinformatics Research and Development (BIRD), Japan Science and Technology Agency (JST), Tokyo, Japan
FreClu funding source(s)
This work was supported in part by a Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Culture, Sports, Science and Technology of Japan, and by a grant for Bioinformatics Research and Development (BIRD) from the Japan Science and Technology Agency (JST).

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