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chevron_left Gene prediction Gene orthology prediction Phylogenetic inference Read quality control Bioinformatics workflows Reference-based transcriptome assembly Transcriptome annotation chevron_right
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Agalma specifications

Information


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
Requirements
BioLite
Maintained Yes

Subtool


  • treeinform

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Versioning


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Documentation


Maintainers


  • person_outline August Guang <>
  • person_outline 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

Publications for Agalma

Agalma in pipeline

2017
PMCID: 5795342
PMID: 29186447
DOI: 10.1093/gigascience/gix116

[…] gene tree was built with raxml software, version 8.0.20 (raxml, rrid: scr_006086), by implementing the maximum likelihood method (ml) []. to infer orthologous genes, we used treeprune in the agalma package [] to mask the monophyletic sequences. we pruned the paralogous subtrees from the homologous gene trees until only 1 monophyletic subtree was retained. next, the resulting orthologous […]


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Agalma in publications

 (18)
PMCID: 5932825
DOI: 10.1186/s12862-018-1142-0

[…] ceriantharia and several other previously under-sampled cnidarian clades to the construction and analyses of independent phylogenomic datasets for cnidaria using two popular approaches: 1) agalma [] and 2) a custom pipeline based on orthofinder [] and phylotreepruner []. we show that both procedures produce datasets with surprisingly little overlap in terms of data composition, […]

PMCID: 5717846
PMID: 29207942
DOI: 10.1186/s12862-017-1071-3

[…] the reproductive medusae (gonophores) remain as part of the colonies. we classified three species that have gonophores of both sexes within one colony as hermaphroditic (ablylopsis tetragona, agalma elegans, and nanomia bijunga) [, ]. we found contradictory reports for the sexual mode of membranipora membranacae [, ]; therefore, we coded this species as unknown. the species anemonia […]

PMCID: 5795342
PMID: 29186447
DOI: 10.1093/gigascience/gix116

[…] gene tree was built with raxml software, version 8.0.20 (raxml, rrid: scr_006086), by implementing the maximum likelihood method (ml) []. to infer orthologous genes, we used treeprune in the agalma package [] to mask the monophyletic sequences. we pruned the paralogous subtrees from the homologous gene trees until only 1 monophyletic subtree was retained. next, the resulting orthologous […]

PMCID: 5648822
PMID: 29051622
DOI: 10.1038/s41598-017-13236-z

[…] blast and/or mcl, but additionally use the topological features of phylogenetic trees to differentiate between orthologs and paralogs,–. two of the most advanced platforms for doing this are the agalma and yang & smith pipelines,,–. these phylogenetically-informed methods have proven effective and become popular in large part because they are computationally tractable […]

PMCID: 5850498
PMID: 29040657
DOI: 10.1093/molbev/msx269

[…] on an illumina hiseq 2500 platform with 100 cycles in rapid mode generating 100 bp paired-end reads, at the sheffield diagnostic genetics service., reads were filtered and assembled using the agalma pipeline version 0.5.0, with default parameters (). this pipeline removes low quality reads (q < 33), and those that are adaptor-contaminated or correspond to ribosomal rna. the filtered […]


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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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