[request] mafft function

[Andreas-Bio]

Are you still maintaining the CRAN version?

Can you please add the option to mafft to add options freely?
I really need the --unalignlevel --allowshift --keeplength options, but I have to fix() it every time.

[FranzKrah]

If you already coded the solution, please just mail to us, then we can include.
Cheers, Franz

[Andreas-Bio]

I just removed this part from the function:

else {
    options <- match.arg(options, c("--adjustdirection", 
                                    "--adjustdirectionaccurately"))
    options <- paste(options, collapse = " ")
}

Which enables me to pass options via the option parameter of the function like this: options= "--thread 4 --adjustdirection --nwildcard"

This may be less user friendly because it will not catch spelling errors in, for example --adjustdirectionaccurately, however it will give more experienced users more flexibility. Then again it's not that bad, because if mafft is supplied with a mispelled parameter it crashes instantly.

This is just my personal opinion.