A partitioned RAD visualization method to investigate the possibility that suboptimal topologies supported by large numbers of loci—due, for example, to reticulate evolution or lineage sorting—are masked by the globally optimal tree. RADami implements import, export, manipulation, visualization, and downstream (post-clustering) analysis of RADseq data, integrating with the pyRAD package.

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RADami classification

RADami specifications

Software type:
Package
Restrictions to use:
None
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Operating system:
Windows
Version:
1.0-3
Source code URL:
https://cran.r-project.org/src/contrib/RADami_1.0-3.tar.gz

Publications

  • (Hipp et al., 2014) A framework phylogeny of the American oak clade based on sequenced RAD data. PLoS One.
    PMID: 24705617

RADami support

Documentation

Credits

Institution(s)

The Morton Arboretum, Lisle, IL, USA; The Field Museum, Department of Botany, Chicago, IL, USA; University of Chicago, Committee on Evolutionary Biology, Chicago, IL, USA; University of Minnesota, College of Biological Sciences, Saint Paul, MN, USA; Floragenex, Inc., Eugene, OR, USA; Duke University, Department of Biology, Durham, NC, USA

Funding source(s)

This work was supported by U.S. National Science Foundation DEB Awards #1146488, #1146380, and #1146102, and a Field Museum Lester Armour Graduate fellowship.

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