Agalma: an automated phylogenomics workflow

@article{Dunn2013AgalmaAA,
  title={Agalma: an automated phylogenomics workflow},
  author={C. Dunn and Mark Howison and F. Zapata},
  journal={BMC Bioinformatics},
  year={2013},
  volume={14},
  pages={330 - 330}
}
  • C. Dunn, Mark Howison, F. Zapata
  • Published 2013
  • Computer Science, Biology, Medicine
  • BMC Bioinformatics
  • BackgroundIn the past decade, transcriptome data have become an important component of many phylogenetic studies. They are a cost-effective source of protein-coding gene sequences, and have helped projects grow from a few genes to hundreds or thousands of genes. Phylogenetic studies now regularly include genes from newly sequenced transcriptomes, as well as publicly available transcriptomes and genomes. Implementing such a phylogenomic study, however, is computationally intensive, requires the… CONTINUE READING
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    References

    SHOWING 1-10 OF 35 REFERENCES
    Assessing the root of bilaterian animals with scalable phylogenomic methods
    • 663
    • PDF
    PartiGene-constructing partial genomes
    • 147
    • PDF
    Large-scale sequencing and the new animal phylogeny.
    • 144
    • PDF
    Higher-level metazoan relationships: recent progress and remaining questions
    • 244
    • PDF
    RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
    • 8,572
    • PDF
    Broad phylogenomic sampling improves resolution of the animal tree of life
    • 1,664
    • PDF
    Full-length transcriptome assembly from RNA-Seq data without a reference genome.
    • 10,907
    • PDF
    DendroPy: a Python library for phylogenetic computing
    • 1,147
    • PDF
    Genome-scale coestimation of species and gene trees.
    • 231
    • PDF
    Inferring ancient divergences requires genes with strong phylogenetic signals
    • 495
    • PDF