id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
work_kwuwhxyuhrdghduymgc3bhsk6q	Orlando Schwery	MonoPhy: a simple R package to find and visualize monophyly issues	2016	8	.pdf	application/pdf	3215	348	58	The monophyly of taxa is an important attribute of a phylogenetic tree. Keywords Phylogeny, Evolution, Monophyly, R package, Taxonomy, Rogue taxa, Tree conflict, How to cite this article Schwery and O'Meara (2016), MonoPhy: a simple R package to find and visualize monophyly issues. for assessing monophyly of taxa in a given phylogeny. from assessing monophyly for all groups and focal taxonomic levels in a tree at once, AssessMonophyly Runs the main analysis to assess monophyly of groups on a tree. GetIntruderTaxa Returns lists of taxa that cause monophyly issues for another taxon. GetIntruderTips Returns lists of tips that cause monophyly issues for a taxon. GetOutlierTaxa Returns lists of taxa that have monophyly issues due to outliers. GetOutlierTips Returns lists of tips that cause monophyly issues for their taxon by being CRAN: https://cran.r-project.org/package=MonoPhy/ Supplemental information for this article can be found online at http://dx.doi.org/10.7717/ https://cran.r-project.org/package=MonoPhy/ https://cran.r-project.org/package=MonoPhy/ http://dx.doi.org/10.7717/peerj-cs.56#supplemental-information http://dx.doi.org/10.7717/peerj-cs.56#supplemental-information	./cache/work_kwuwhxyuhrdghduymgc3bhsk6q.pdf	./txt/work_kwuwhxyuhrdghduymgc3bhsk6q.txt