Hello,

I want to align multiple FASTA files in a directory with MAFFT.

Is it correct to do this with `parallel`(where `--thread n` is the maximum number of cores in the machine):

`ls *.fasta | parallel 'mafft --adjustdirection --thread n {} > {.}_mafft.fasta'`

If I am interpreting the line above correctly, each alignment will be performed in parallel using the maximum number of cores possible. Am I correct in setting the `--thread` option to the maximum number of cores for each alignment, or is `parallel` already taking care of that?

Or is it preferable to perform something like the for loop below and align the FASTA files sequentially:

    for i in *.fasta; do
    mafft --adjustdirection --thread n ${i} > ${i%.*}_mafft.fasta;
    done

Thanks.

It would be more efficient to do the alignments sequentially using the maximum number of cores you have available (since you are able to use multiple threads). If you started multiple parallel jobs (each with multiple cores) they would compete for the same cores and the jobs would bog each other down.