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#' Create a random alignment
#' @inheritParams default_params_doc
#' @param sequence_length The number of base pairs the alignment will have
#' @param rate mutation rate
#' @param taxa_name_ext the extension of the taxa names
#' @return an alignment of class \link[ape]{DNAbin}
#' @author Richèl J.C. Bilderbeek
#' @examples
#' check_empty_beaustier_folders()
#'
#' alignment <- create_random_alignment(
#' n_taxa = 5,
#' sequence_length = 10
#' )
#' image(alignment)
#'
#' remove_beaustier_folders()
#' check_empty_beaustier_folders()
#' @export
create_random_alignment <- function(
n_taxa,
sequence_length,
rate = 1,
taxa_name_ext = ""
) {
if (n_taxa < 2) {
stop("need n_taxa >= 2")
}
if (sequence_length < 1) {
stop("need sequence_length >= 1")
}
if (rate < 0.0 || rate > 1.0) {
stop("rate needs to be [0.0, 1.0]")
}
phylogeny <- create_random_phylogeny(
n_taxa = n_taxa,
taxa_name_ext = taxa_name_ext
)
alignments_phydat <- phangorn::simSeq(
phylogeny, l = sequence_length, rate = rate
)
alignments_dnabin <- ape::as.DNAbin(alignments_phydat)
alignments_dnabin
}
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