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

Share:

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.

Author
Orlando Schwery
Date of publication
2016-07-26 17:48:01
Maintainer
Orlando Schwery <oschwery@vols.utk.edu>
License
GPL-3
Version
1.2

View on CRAN

Man pages

AssessMonophyly
Assesses monophyly (or lack of it) of taxonomic groups in a...
GetAncNodes
Get MRCA nodes of taxonomic groups from 'AssessMonophyly'...
GetIntruderTaxa
Get taxa or tips which are intruders or outliers to a taxon...
GetResultMonophyly
Get main result table from 'AssessMonophyly' output
MonophylyData
Example dataset for the package MonoPhy.
MonoPhy-package
Allows to explore monophyly (or lack of it) of taxonomic...
PlotMonophyly
Plot output of AssessMonophyly

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