clean_dna: Removes Gaps, Ambiguities and Missing Data from DNA Sequences
Description
clean_dna() removes all character not a valid ACTG base from a DNAbin
object.
Usage
clean_dna(dna, verbose = TRUE)
Value
an object of class DNAbin.
Arguments
dna
an object of class DNAbin.
verbose
logical. Returns a warning if any sequence contains non ACTG bases.
Author
Rupert A. Collins
Details
clean_dna() detects and removes any non ACTG bases from alignment. This includes:
"N", "-", "?", "R", "Y", etc. If verbose = TRUE, returns a warning if these characters
are inside the sequences, i.e, are not alignment padding chars at the ends.