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Fun4Me specifications


Unique identifier OMICS_19592
Name Fun4Me
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Takes a query metagenomic dataset (of either short sequencing reads, or assemblies).
Output data Putative protein-coding genes or gene fragments, their putative functions in Gene Ontology (GO) terms or EC numbers, and possible metabolic pathways.
Operating system Unix/Linux
Programming languages C++, Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Yuzhen Ye <>
  • person_outline Fatemeh Sharifi <>

Publication for Fun4Me

Fun4Me in publication

PMCID: 5829635
PMID: 29194524
DOI: 10.1093/nar/gkx1209

[…] were removed as uninformative (<1% of total e.c.s in both cases). the correlation between samples was calculated with spearman's rho, ρ, offered in the r package, hmisc ()., two other tools, fun4me and shotmap, were installed locally and run on the artificial metagenome with default parameters; for both, we compared the precision of the methods (equation ) as well as the number […]

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Fun4Me institution(s)
School of Informatics and Computing, Indiana University, Bloomington, IN, USA
Fun4Me funding source(s)
Supported by NIH grant 1R01AI108888 and NSF grant DBI-0845685.

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