insertBC: Insert barcodes in an alignment
In fkeck/diatobc: Bioinformatic toolbox for my projects

Description Usage Arguments Value

This function inserts new barcodes into an alignment. For this purpose, the barcode region of the reference alignment is re-aligned with the new set of barcodes.

1 2	insertBC(bc, ref, region, align.method = "mafft", align.exec = NULL, threads = NULL, trim = FALSE)

`bc`	barcodes sequences. A `DNAbin` object or a path of a sequence file to be read in fasta format.
`ref`	the reference alignment. A `DNAbin` object or a path of a sequence file to be read in fasta format.
`region`	a vector of two integers giving the boundaries of the barcodes region within the reference alignment.
`align.method`	a character string giving the method to use for alignment. Available methods are "`mafft`", "`muscle`" and "`none`" (to avoid alignment step).
`align.exec`	a character string giving the path of the program if necessary.
`threads`	an integer giving the number of threads to use. Available only with mafft.
`trim`	logical. If `TRUE`, only the barcode region is returned.