MetaFlow specifications


Unique identifier OMICS_11124
Name MetaFlow
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data There are two input files for the tool: (i) a mapping file: this is the aligner’s output file converted into another format which is easier to process by MetaFlow; (ii) a species database file: a file containing the names and lengths of the genomes in the reference database.
Output data MetaFlow generates different output files. All the files are in CSV format to make any further analysis easy.
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 0.9.1
Stability Stable
Maintained Yes




No version available


  • person_outline Alexandru Tomescu

Publication for MetaFlow

MetaFlow citation


Dynamic Zebrafish Interactome Reveals Transcriptional Mechanisms of Dioxin Toxicity

PLoS One
PMCID: 2864754
PMID: 20463971
DOI: 10.1371/journal.pone.0010465

[…] scriptional regulation. Relatively few calcium-related proteins were identified on day 1; two examples were cab39 and heg. While the CYP1A neighborhood itself was not heavily altered on day 1, it had metaflow GO category connections “day 1→day 2” to “calcium ion transport”. In particular, although none of calmodulins were dioxin-regulated on day 1, eight of them were strongly over-expressed later, […]

MetaFlow institution(s)
Helsinki Institute for Information Technology HIIT, Helsinki, Finland; Department of Computer Science, University of Helsinki, Helsinki, Finland
MetaFlow funding source(s)
This work was partially supported by the Academy of Finland under grants 284598 (CoECGR) and 274977.

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