replicate {insect}

Dereplicate and rereplicate sequence datasets.

Description

These functions are used to extract only the unique sequences from a set of DNA reads, with the ability to rebuild the original sequence set at a later time.

Usage

dereplicate(x, cores = 1)

rereplicate(x)

Arguments

x

a list of sequences in DNAbin or AAbin format, or a vector of sequences as concatenated upper-case character strings.

cores

integer giving the number of processors for multithreading (defaults to 1). This argument may alternatively be a 'cluster' object, in which case it is the user's responsibility to close the socket connection at the conclusion of the operation, e.g. by running parallel::stopCluster(cores). The string 'autodetect' is also accepted, in which case the maximum number of cores to use is one less than the total number of cores available.

Value

either a DNAbin/AAbin object, or a vector of concatenated upper-case character strings, depending on the input object.

Author(s)

Shaun Wilkinson

Examples

  data(whales)
  tmp <- dereplicate(whales)
  whales <- rereplicate(tmp)