get_subalignment: Get subalignment

In alexpiper/taxreturn: An R package for retrieving and curating public DNA barcode reference data

Get subalignment

Description

Aligns a DNABin to a reference PHMM model, and returns the optimal path

Usage

get_subalignment(
  x,
  model,
  tryrc = FALSE,
  quiet = FALSE,
  check_indels = TRUE,
  min_score = 10,
  omit_endgaps = FALSE,
  multithread = 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.
tryrc	Whether the reverse complement should also be aligned
quiet	Whether progress should be printed to the console.
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
...	aditional arguments to be passed to "Viterbi"

alexpiper/taxreturn documentation built on Sept. 14, 2024, 7:56 p.m.