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FunFrame

Uses algorithms to de-noise functional gene pyrosequences and performs ecological analysis on de-noised sequence data. FunFrame is an R-based data-analysis pipeline which provides users a unified set of tools, adapted from disparate sources and designed for different applications, that can be used to examine a particular protein coding gene of interest. FunFrame reduced spurious diversity while retaining more sequences than a commonly used de-noising method that discards sequences with frameshift errors.

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FunFrame classification

FunFrame specifications

Software type:
Pipeline/Workflow
Restrictions to use:
None
Programming languages:
Python, R, Shell (Bash)
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Operating system:
Unix/Linux
License:
GNU General Public License version 3.0
Version:
0.9.3
Maintained:
Yes

FunFrame distribution

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FunFrame support

Maintainer

  • Jennifer Bowen <>

Credits

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Publications

Institution(s)

Department of Biology, University of Massachusetts Boston, Boston, MA, USA

Funding source(s)

This work was supported by the National Science Foundation (DEB-0717155 and DBI-0400819) and by the University of Massachusetts of Boston.

Link to literature

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