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Supplemental Information

Supplementary Information: Commands for Examples (MonoPhy)

The commented R commands to run the examples from the main article, along with the detailed results.

DOI: 10.7287/peerj.preprints.1600v1/supp-1

Monophyly plot of the genera of Ericaceae

Fig. S1: Monophyly plot of the genera of Ericaceae, with branches of the tree coloured by monophyly status. We see clearly how e.g.Orthilia invades Pyrola and how Vaccinium has two outliers.

DOI: 10.7287/peerj.preprints.1600v1/supp-2

Monophyly plot of the genera of Embryophyta, collapsed

Fig. S2: Monophyly plot of the genera of Embryophyta, with branches of the tree coloured by monophyly status, just as in Figure 1. Monophyletic groups were collapsed to one branch to save space.

DOI: 10.7287/peerj.preprints.1600v1/supp-3

Monophyly plot of the genera of Embryophyta, uncollapsed

Fig. S3: Monophyly plot of the genera of Embryophyta, with branches of the tree coloured by monophyly status, just as in Figure 1. Monophyletic groups were not collapsed to one branch.

DOI: 10.7287/peerj.preprints.1600v1/supp-4

Intruder plot of the genera of Embryophyta

Fig. S4: Intruder plot of the genera of Embryophyta, with branches of the tree coloured by monophyly status (monophyletic gray, non-monophyletic black) and intruders and outliers coloured according to their genus. Monophyletic groups were not collapsed to one branch.

DOI: 10.7287/peerj.preprints.1600v1/supp-5

MonoPhy results of Embryophyta

Tab. S1:MonoPhy result table for the genera of Ericaceae.

DOI: 10.7287/peerj.preprints.1600v1/supp-6

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Orlando Schwery conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, performed the computation work.

Brian C O'Meara contributed reagents/materials/analysis tools, wrote the paper.

Data Deposition

The following information was supplied regarding data availability:

CRAN https://cran.r-project.org/package=MonoPhy/

GitHub https://github.com/oschwery/MonoPhy

Funding

This work has been supported via a GTA to O.S. by the University of Tennessee, Knoxville. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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