mites: Morphological characters of Mites (Schäffer et al. 2010)

In phangorn: Phylogenetic Reconstruction and Analysis

Morphological characters of Mites (Schäffer et al. 2010)

Description

Matrix for morphological characters and character states for 12 species of mites. See vignette '02_Phylogenetic trees from morphological data' for examples to import morphological data.

References

Schäffer, S., Pfingstl, T., Koblmüller, S., Winkler, K. A., Sturmbauer, C., & Krisper, G. (2010). Phylogenetic analysis of European Scutovertex mites (Acari, Oribatida, Scutoverticidae) reveals paraphyly and cryptic diversity: a molecular genetic and morphological approach. Molecular Phylogenetics and Evolution, 55(2), 677–688.

Examples

data(mites)
mites
# infer all maximum parsimony trees
trees <- bab(mites)
# For larger data sets you might use pratchet instead bab
# trees <- pratchet(mites, minit=200, trace=0, all=TRUE)
# build consensus tree
ctree <- root(consensus(trees, p=.5), outgroup = "C._cymba",
              resolve.root=TRUE, edgelabel=TRUE)
plotBS(ctree, trees)
cnet <- consensusNet(trees)
plot(cnet)

phangorn documentation built on Sept. 17, 2024, 5:08 p.m.