MonoPhy: Allows to Explore Monophyly (or Lack of it) of Taxonomic Groups in a Phylogeny

Requires rooted resolved 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.

AuthorOrlando Schwery
Date of publication2016-07-26 17:48:01
MaintainerOrlando Schwery <oschwery@vols.utk.edu>
LicenseGPL-3
Version1.2

View on CRAN

Files in this package

MonoPhy
MonoPhy/inst
MonoPhy/inst/CITATION
MonoPhy/inst/doc
MonoPhy/inst/doc/MonoPhyVignette.Rmd
MonoPhy/inst/doc/MonoPhyVignette.html
MonoPhy/inst/doc/MonoPhyVignette.R
MonoPhy/tests
MonoPhy/tests/testthat.R
MonoPhy/tests/testthat
MonoPhy/tests/testthat/test_solutions.R
MonoPhy/NAMESPACE
MonoPhy/data
MonoPhy/data/Ericactree.rda
MonoPhy/data/Ericacsubfams.rda
MonoPhy/data/Ericactribes.rda
MonoPhy/R
MonoPhy/R/GetSummaryMonophyly.R MonoPhy/R/PlotMonophyly.R MonoPhy/R/GetIntruderTaxa.R MonoPhy/R/GetOutlierTips.R MonoPhy/R/GetAncNodes.R MonoPhy/R/AssessMonophyly.R MonoPhy/R/GetOutlierTaxa.R MonoPhy/R/GetIntruderTips.R MonoPhy/R/GetResultMonophyly.R
MonoPhy/vignettes
MonoPhy/vignettes/MonoPhyVignette.Rmd
MonoPhy/README.md
MonoPhy/MD5
MonoPhy/build
MonoPhy/build/vignette.rds
MonoPhy/DESCRIPTION
MonoPhy/man
MonoPhy/man/PlotMonophyly.Rd MonoPhy/man/MonoPhy-package.Rd MonoPhy/man/AssessMonophyly.Rd MonoPhy/man/GetResultMonophyly.Rd MonoPhy/man/MonophylyData.Rd MonoPhy/man/GetIntruderTaxa.Rd MonoPhy/man/GetAncNodes.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.