muscle_par: Copy of muscle function from ape package with tweaks to allow...

Description Usage Arguments

View source: R/align_sequences.R

Description

Copy of muscle function from ape package with tweaks to allow parallel execution

Usage

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muscle_par(x, exec = "muscle", MoreArgs = "", quiet = TRUE,
  original.ordering = TRUE, keep_alignment_files = FALSE)

Arguments

x

an object of class ‘"DNAbin"’.

exec

a character string giving the name of the program, with its path if necessary. ‘clustal’ tries to guess it depending on the operating system (see details).

MoreArgs

a character string giving additional options.

quiet

a logical: the default is to not print on R's console the messages from the external program.

original.ordering

a logical specifying whether to return the aligned sequences in the same order than in ‘x’.

keep_alignment_files

Default is FALSE. If set to TRUE, then the files produced by muscle will not be deleted.

pw.gapopen

gap opening and gap extension penalties used by Clustal during pairwise alignments.

pw.gapext

gap opening and gap extension penalties used by Clustal during pairwise alignments.

gapopen

idem for global alignment.

gapext

idem for global alignment.


philliplab/MotifBinner documentation built on Sept. 2, 2020, 11:41 a.m.