Agalma

Agalma is a software tool for creating matrices from raw Illumina transcriptome data or assembled genomes or transcriptomes. The Agalma has functions for making annotated assemblies, aligned gene sequence matrices, and constructing preliminary phylogeny and species trees. It also produces detailed diagnostics for extensive assessments. Agalma uses the BioLite bioinformatics framework.

Topic

Transcriptomics;Genomics;Phylogenomics

Detail

  • Operation: Sequence assembly;Transcriptome assembly

  • Software interface: Command-line user interface

  • Language: Python

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 2.0.0

  • Credit: The US National Science Foundation

  • Input: FASTQ

  • Output: JSON

  • Contact: Casey W Dunn casey_dunn@brown.edu, Mark Howison mhowison@brown.edu, Felipe Zapata felipe_zapata@brown.edu

  • Collection: -

  • Maturity: -

Publications

  • Agalma: an automated phylogenomics workflow.
  • Dunn CW, Howison M, Zapata F. Agalma: an automated phylogenomics workflow. BMC Bioinformatics. 2013 Nov 19;14:330. doi: 10.1186/1471-2105-14-330. PMID: 24252138; PMCID: PMC3840672.
  • https://doi.org/10.1186/1471-2105-14-330
  • PMID: 24252138
  • PMC: PMC3840672

Download and documentation

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