MonoPhy

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R package to explore monophyly

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- Ericacsubfams.rda
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- Ericactribes.rda
- CITATION
- - logo.png
  - logo1.png
  - logo2.png
  - logo3.png
  - logo4.png
  - logo5.png
- AssessMonophyly.Rd
- CollapseMonophyletics.Rd
- GetAncNodes.Rd
- GetIntruderTaxa.Rd
- GetResultMonophyly.Rd
- MonoPhy-package.Rd
- MonophylyData.Rd
- PlotMonophyly.Rd
- AssessMonophyly.R
- CollapseMonophyletics.R
- GetAncNodes.R
- GetIntruderTaxa.R
- GetIntruderTips.R
- GetOutlierTaxa.R
- GetOutlierTips.R
- GetResultMonophyly.R
- GetSummaryMonophyly.R
- MonoColl.R
- PlotMonophyly.R
- - test_solutions.R
- .DS_Store
- testthat.R
- MonoPhyVignette.Rmd
.Rbuildignore
.travis.yml
DESCRIPTION
NAMESPACE
README.md

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## Explore Monophyly of Taxonomic Groups in a Phylogeny
R package to explore monophyly (or lack thereof) of taxonomic groups in a phylogenetic tree.
Requires rooted phylogeny as input and creates a table of genera, their monophyly-status, which taxa cause problems in monophyly etc.Different information can be extracted from the output and a plot function allows visualization of the results in a number of ways.

Usage instructions can be found in the manual and [tutorial vignette](https://cran.r-project.org/web/packages/MonoPhy/vignettes/MonoPhyVignette.html).
This is the developing branch, a stable version can be found on [**CRAN**](https://cran.r-project.org/web/packages/MonoPhy/index.html).

**Citation**:  
Schwery, O. & O'Meara, B.C. (**2016**), _MonoPhy_: a simple R package to find and visualize monophyly issues. _PeerJ Computer Science_ 2:e56. [10.7717/peerj-cs.56](https://doi.org/10.7717/peerj-cs.56)

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MonoPhy

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