View source: R/align_sequences.R
Copy of muscle function from ape package with tweaks to allow parallel execution
1 2 | muscle_par(x, exec = "muscle", MoreArgs = "", quiet = TRUE,
original.ordering = TRUE, keep_alignment_files = FALSE)
|
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. |
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