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  • 1. Aberer, André
    et al.
    Stamatakis, Alexis
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    An efficient independence sampler for updating branches in Bayesian Markov chain Monte Carlo sampling of phylogenetic trees2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 1, p. 161-176Article in journal (Refereed)
  • 2.
    Hsiang, Allison
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Elder, Leanne (Contributor)
    Yale University.
    Sibert, Elizabeth (Contributor)
    Harvard University.
    Kahanamoku, Sara (Contributor)
    University of California, Berkeley.
    Burke, Janet (Contributor)
    Yale University.
    Kelly, Abigail (Contributor)
    Smithsonian Tropical Research Institute.
    Liu, Yusu (Contributor)
    Massachusetts Institute of Technology.
    Hull, Pincelli (Contributor)
    Yale University.
    AutoMorph: Accelerating morphometrics with automated 2D and 3D image processing and shape extraction2017In: Methods in Ecology and Evolution, ISSN 2041-210X, EISSN 2041-210XArticle in journal (Refereed)
    Abstract [en]
    1. Large-scale, comparative studies of morphological variation are rare due to the time-intensive nature of shape quantification. This data gap is important to address, as intraspecific and interspecific morphological variation underpins and reflects ecological and evolutionary processes.

    2. Here, we detail a novel software package, AutoMorph, for high-throughput object and shape extraction. AutoMorph can batch image many types of organisms (e.g. foraminifera, molluscs and fish teeth), allowing for rapid generation of assemblage- scale morphological data.

    3. We used AutoMorph to image and generate 2D and 3D morphological data for >100,000 marine microfossils in about a year. Our collaborators have used AutoMorph to process >12,000 patellogastropod shells and >50,000 fish teeth.

    4. AutoMorph allows users to rapidly produce large amounts of morphological data, facilitating community-scale evolutionary and ecological studies. To hasten the adoption of automated approaches, we have made AutoMorph freely available and open source. AutoMorph runs on all UNIX-like systems; future versions will run across all platforms. 

  • 3. Höhna, Sebastian
    et al.
    Landis, Michael J.
    Heath, Tracy A.
    Boussau, Bastien
    Lartillot, Nicolas
    Moore, Brian R.
    Huelsenbeck, John P.
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 4, p. 726-736Article in journal (Refereed)
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