hypermutR: Detects hypermutation in DNA

#' Low diversity sequence sample
#'
#' The HVTN 503/Phambili study (Gray et al. Lancet Infect Dis. 2011) followed
#' HIV negative subjects monitoring for HIV-1 infection. To produce
#' this dataset, we took the PID Illumina MiSeq sequence data from the sample
#' HVTN503-162400146-1011 and built phylogenetic trees with RAxML. The
#' following RAxML settings were used:
#' \describe{
#'   \item{-f a}{Perform rapid bootstrap analysis and search for the best-scoring maximum likelihood tree in one program run.}
#'   \item{-x 12345}{Seed for the random number generator used by the rapid bootstrap analysis.}
#'   \item{-p 12345}{Seed for the random number generator used in the parsimony inferences.}
#'   \item{-# 100}{The number of bootstrap analyses to run on distinct starting trees.}
#'   \item{-m GTRGAMMA}{The model used for the nucleotide substitutions. The general time reversible model with optimization of the substitution rates and the GAMMA model of rate heterogeneity.}
#' }
#' Using the tree produced by RAxML, a random subtype-C sequence was selected
#' (referred to as the seed sequence) from LANL (C.ZA.08.707PKE34F2.HM623575),
#' restricted to the same amplicon as the real dataset and mutated according to
#' these trees.  To simulate test data, the tree was loaded into R in a
#' data.frame in which each row represents an edge. The data.frame contains
#' three columns, the first one lists the ancestor, the second one lists
#' the descendant and the last one the length of the edge. The simulation is
#' initiated by assigning the seed sequence to the descendant in the first row
#' of the dataset. The ancestor is then constructed by randomly mutating the
#' seed sequence until it diverged by the edge length. The newly simulated
#' ancestor sequence is then used to generate the other sequences that are
#' directly related to it. This process is continued until all the sequences in
#' the entire tree (including the internal nodes) are generated.
#'
#' @format A SeqFastadna object from library seqinr
#' @source Based on sample HVTN503-162400146-1011 from the HVTN 503/Phambili study (Gray et al. Lancet Infect Dis. 2011).
"ld_seqs"

#' High diversity sequence sample
#'
#' The HVTN 503/Phambili study (Gray et al. Lancet Infect Dis. 2011) followed
#' HIV negative subjects monitoring for HIV-1 infection. To produce
#' this dataset, we took the PID Illumina MiSeq sequence data from the sample
#' HVTN503-162450071-1056 and built phylogenetic trees with RAxML. The
#' following RAxML settings were used:
#' \describe{
#'   \item{-f a}{Perform rapid bootstrap analysis and search for the best-scoring maximum likelihood tree in one program run.}
#'   \item{-x 12345}{Seed for the random number generator used by the rapid bootstrap analysis.}
#'   \item{-p 12345}{Seed for the random number generator used in the parsimony inferences.}
#'   \item{-# 100}{The number of bootstrap analyses to run on distinct starting trees.}
#'   \item{-m GTRGAMMA}{The model used for the nucleotide substitutions. The general time reversible model with optimization of the substitution rates and the GAMMA model of rate heterogeneity.}
#' }
#' Using the tree produced by RAxML, a random subtype-C sequence was selected
#' (referred to as the seed sequence) from LANL (C.ZA.08.707PKE34F2.HM623575),
#' restricted to the same amplicon as the real dataset and mutated according to
#' these trees. To simulate test data, the tree was loaded into R in a
#' data.frame in which each row represents an edge. The data.frame contains
#' three columns, the first one lists the ancestor, the second one lists
#' the descendant and the last one the length of the edge. The simulation is
#' initiated by assigning the seed sequence to the descendant in the first row
#' of the dataset. The ancestor is then constructed by randomly mutating the
#' seed sequence until it diverged by the edge length. The newly simulated
#' ancestor sequence is then used to generate the other sequences that are
#' directly related to it. This process is continued until all the sequences in
#' the entire tree (including the internal nodes) are generated. Extra variability 
#' was introduced into this dataset by multiplying all the branch lengths by 2.
#'
#' @format A SeqFastadna object from library seqinr
#' @source Based on sample HVTN503-162450071-1056 from the HVTN 503/Phambili study (Gray et al. Lancet Infect Dis. 2011).
"hd_seqs"