R/data.R

In domingoscardoso/catGenes: Concatenating multiple DNA alignments and other phylogenetic features

#' @name Luetzelburgia
#'
#' @docType data
#'
#' @title DNA alignments of the legume genus Luetzelburgia
#'
#' @description List of nine individual DNA alignments of the neotropical legume genus
#' Luetzelburgia, containing nuclear ribossomal (ETS, ITS) and plastid
#' (matK, psbA-trnH, rpS16, trnD-T, trnK intron, trnL intron, trnQ) genes.
#'
#' @format DNA sequences in NEXUS format as read by ape's function \code{\link{read.nexus.data}}.
#'
#' @source <https://onlinelibrary.wiley.com/doi/10.12705/675.6>
#'
#' @usage data(Luetzelburgia)

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#' @name Vataireoids
#'
#' @docType data
#'
#' @title DNA alignments of the Vataireoid legumes
#'
#' @description List of eight individual DNA alignments of the neotropical Vataireoid legumes,
#' containing nuclear ribossomal (ETS, ITS) and plastid (matK, psbA-trnH, rpS16,
#' trnD-T, trnL intron, trnQ) genes.
#'
#' @format DNA sequences in NEXUS format as read by ape's function \code{\link{read.nexus.data}}.
#'
#' @source <https://bsapubs.onlinelibrary.wiley.com/doi/10.3732/ajb.1200276>
#'
#' @usage data(Vataireoids)

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#' @name Brongniartia
#'
#' @docType data
#'
#' @title DNA alignments of the papilionid legume genus Brongniartia
#'
#' @description List of three individual DNA alignments of the predominantly Mesoamerican genus
#' Brongniartia of papilinoid legumes, containing
#' nuclear ribossomal (ITS, ETS) and plastid (matK, trnLF) genes.
#'
#' @format DNA sequences in NEXUS format as read by ape's function \code{\link{read.nexus.data}}.
#'
#' @source Dorado, Snak, São-Mateus, Delgado-Salinas, Queiroz  & Cardoso (unpubl. data)
#'
#' @usage data(Brongniartia)

NULL

#' @name Ormosia
#'
#' @docType data
#'
#' @title DNA alignments of the pantropical legume genus Ormosia
#'
#' @description List of four individual DNA alignments of the pantropical papilionoid legume
#' genus Ormosia, containing nuclear ribossomal (ITS) and plastid (matK, trnK intron,
#' trnLF) genes.
#'
#' @format DNA sequences in NEXUS format as read by ape's function \code{\link{read.nexus.data}}.
#'
#' @source <https://bsapubs.onlinelibrary.wiley.com/doi/10.3732/ajb.1200276>
#'
#' @usage data(Ormosia)

NULL

#' @name Gaya
#'
#' @docType data
#'
#' @title DNA alignments of the genus Gaya (Malvaceae)
#'
#' @description List of three individual DNA alignments of the neotropical genus
#' Gaya (Malvaceae), containing nuclear ribossomal (ITS) and plastid (petL-psbE, rpL16) genes.
#'
#' @format DNA sequences in NEXUS format as read by ape's function \code{\link{read.nexus.data}}.
#'
#' @source <https://www.ingentaconnect.com/content/aspt/sb/2018/00000043/00000003/art00004;jsessionid=20r008g64rupe.x-ic-live-02>
#'
#' @usage data(Gaya)

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#' @name Cryptocarya
#'
#' @docType data
#'
#' @title DNA alignments of the genus Cryptocarya (Lauraceae)
#'
#' @description List of four individual DNA alignments of the pantropical genus
#' Cryptocarya (Lauraceae), containing the nuclear ribossomal (ITS) and plastid
#' (matK, psbA, rbcL) genes.
#'
#' @format DNA sequences in NEXUS format as read by ape's function \code{\link{read.nexus.data}}.
#'
#' @source Moraes, Cardoso, et al. (unpubl. data)
#'
#' @usage data(Cryptocarya)

NULL

#' @name Vochysiaceae
#'
#' @docType data
#'
#' @title Plastome dataset of Vochysiaceae (Myrtales)
#'
#' @description List of 78 protein coding plastid genes for 122 species from Vochysiaceae and
#' seven other families of Myrtales as originally used to investigate the historical biogeography
#' of Vochysiaceae across the Neotropics (Goncalves et al. 2020).
#'
#' @format DNA sequences in NEXUS format as read by ape's function \code{\link{read.nexus.data}}.
#'
#' @source <https://doi.org/10.5061/dryad.sn02v6x1g>
#' @source <https://bsapubs.onlinelibrary.wiley.com/doi/abs/10.1002/ajb2.1502>
#'
#' @usage data(Vochysiaceae)

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#' @name Harpalyce_bayes_tree
#'
#' @docType data
#'
#' @title Bayesian tree of the papilionoid legume genus Harpalyce
#'
#' @description A Bayesian majority rule consensus tree of the  papilionoid legume
#' tribe Brongniartieae with a focus on the genus Harpalyce, based on analysis
#' of combined nuclear (ITS, ETS) and plastid (matK, trnL intron) DNA sequence
#' data.
#'
#' @format A ggtree phylo object as read by treeio's function \code{\link{read.beast}}.
#'
#' @usage data(Harpalyce_bayes_tree)

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#' @name Harpalyce_parsimony_tree
#'
#' @docType data
#'
#' @title Parsimony tree of the papilionoid legume genus Harpalyce
#'
#' @description A boostrap consensus tree of the  papilionoid legume
#' tribe Brongniartieae with a focus on the genus Harpalyce, based on parsimony
#' analysis of combined nuclear (ITS, ETS) and plastid (matK, trnL intron) DNA
#' sequence data.
#'
#' @format A ggtree phylo object as read by treeio's function \code{\link{read.beast}}.
#'
#' @usage data(Harpalyce_parsimony_tree)

NULL

#' @name Harpalyce_raxml_tree
#'
#' @docType data
#'
#' @title RAxML tree of the papilionoid legume genus Harpalyce
#'
#' @description A RAxML tree of the  papilionoid legume tribe Brongniartieae with
#' a focus on the genus Harpalyce, based on maximum likelihood analysis of
#' combined nuclear (ITS, ETS) and plastid (matK, trnL intron) DNA sequence data.
#'
#' @format A ggtree phylo object as read by treeio's function \code{\link{read.raxml}}.
#'
#' @usage data(Harpalyce_raxml_tree)

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#' @name GenBank_accessions
#'
#' @docType data
#'
#' @title Dataframe with GenBank accessions numbers
#'
#' @description Dataframe with representative species of the Randia clade of
#' Rubiaceae and associated voucher information and GenBank accessions numbers
#' for the DNA regions 'ETS', 'ITS', 'matK', 'petBpetD', 'trnTF', and 'Xdh', as
#' well as for some plastomes.
#'
#' @format Dataframe object.
#'
#' @usage data(GenBank_accessions)

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