nuc_cp | R Documentation |
Data set of nuclear and chloroplast loci of 52 orchid taxa from Kew DNA and Tissue Collection, https://dnabank.science.kew.org/homepage.html (Perez-Escobar et al. 2021).
data(nuc_cp)
This data set consists of seven objects:
np_matrix
Associations one-to-one between the 52 orchid taxa. A binary matrix with 52 rows (nuclear) and 52 columns (chloroplast).
NUCtr
Phylogeny constructed by sequence data of nuclear
loci of orchids (Perez-Escobar et al. 2021).
An object of class "phylo"
containing the details of
the phylogenetic tree (i.e. edge, edge length, nodes and tips names).
CPtr
Phylogeny constructed by sequence data of chloroplast
loci of orchids (Perez-Escobar et al. 2021).
An object of class "phylo"
containing the details of
the phylogenetic tree (i.e. edge, edge length, nodes and tips names).
NUC_500tr
500 bootstrap replicates trees from
Perez-Escobar et al. (2021).
Object of class "multiphylo"
containing a 500 phylogenetic trees
with their respective details (i.e. edges, edges length, nodes, and
tips names).
CP_500tr
500 bootstrap replicates trees from
Perez-Escobar et al. (2021).
Object of class "multiphylo"
containing a 500 phylogenetic trees
with their respective details (i.e. edges, edges length, nodes, and
tips names).
pp_treesPACo_cong
Matrix with the value of the PACo statistics generated for each pair (H and S) of posterior probability trees maximizing congruence between them.
pp_treesPACo_incong
Matrix with the value of the PACo statistics generated for each pair (H and S) of posterior probability trees maximizing incongruence between them.
Perez-Escobar O.A., Dodsworth S., Bogarin D., Bellot S., Balbuena J.A., Schley R., Kikuchi I., Morris S.K., Epitawalage N., Cowan R., Maurin O., Zuntini A., Arias T., Serna A., Gravendeel B., Torres M.F., Nargar K., Chomicki G., Chase M.W., Leitch I.J., Forest F., Baker W.J. (2021). Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. American Journal of Botany, 108(7), 1166-1180.
Perez-Escobar O.A., Dodsworth S., Bogarin D., Bellot S., Balbuena J.A., Schley R., Kikuchi I., Morris S.K., Epitawalage N., Cowan R., Maurin O., Zuntini A., Arias T., Serna A., Gravendeel B., Torres M.F., Nargar K., Chomicki G., Chase M.W., Leitch I.J., Forest F., Baker W.J. (2021). Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. American Journal of Botany, 108(7), 1166-1180.
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