Agalma specifications


Unique identifier OMICS_04249
Name Agalma
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Raw Illumina transcriptome data.
Input format FASTQ
Output data Annotated assemblies, aligned gene sequence matrices, a preliminary phylogeny, and detailed diagnostics.
Operating system Unix/Linux, Mac OS
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.0
Stability Stable
Maintained Yes


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  • person_outline August Guang <>
  • person_outline Casey Dunn <>

Additional information Tutorial:

Publications for Agalma

Agalma institution(s)
Division of Applied Mathematics, Brown University, Providence, RI, USA; Computing & Information Services, Brown University, Providence, RI, USA; Department of Ecology & Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA, USA; Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
Agalma funding source(s)
Supported by the National Science Foundation [DGE-0966060], the National Science Foundation (awards OCI-0725070 and ACI-1238993), the state of Illinois and in part by NSF IGERT award DGE-0966060.

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