Pad alignment

Aligns a DNABin to a reference PHMM model, and pads any gaps between the query and reference

pad_alignment(
  x,
  model,
  pad = "-",
  tryrc = FALSE,
  check_indels = TRUE,
  min_score = 10,
  omit_endgaps = FALSE,
  multithread = FALSE,
  quiet = FALSE,
  ...
)

Arguments

x

A DNAbin object or an object coercible to DNAbin

model

A profile hidden Markov model (a "PHMM" object) generated by the aphid R package to align the sequences to.

pad

The character used to pad the gaps

tryrc

Whether the reverse complement should also be aligned

check_indels

Check that indels are multiples of 3, recommended for coding sequences such as COI

min_score

Minimum score for the viterbi alignment

omit_endgaps

Should gap characters at each end of the sequences be ignored when deriving the transition probabilities of the model? Defaults to FALSE. Set to TRUE if x is not a strict global alignment (i.e. if the alignment contains partial sequences with missing sections represented with gap characters).

multithread

Whether multithreading should be used, if TRUE the number of cores will be automatically detected, or provided a numeric vector to manually set the number of cores to use

quiet

Whether progress should be printed to the console.

...

aditional arguments to be passed to "Viterbi"