Agalma specifications

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

Subtools

  • treeinform

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Agalma distribution

download

Agalma support

Documentation

Maintainers

  • August Guang <>
  • Casey Dunn <>

Additional information

https://bitbucket.org/caseywdunn/agalma/wiki/Hom Tutorial: https://bitbucket.org/caseywdunn/agalma/src/master/TUTORIAL.md?fileviewer=file-view-default

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Publications

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

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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