Why running MAFFT take so long?

[Caroline Tochetto]

Hi everyone!

I have a multi-fasta file with 556 sequences and I would like do run SDT with MAFFT but it is very slow. I´m using a MAC.

 Muscle, for instance, is so faster, why? Is there anyway to improve mafft so it can run faster in SDT?

Any tips will be welcome!  :)

Thanks in advance!

Caroline Tochetto.

[Sequence Demarcation Tool SDT users]

Hi Caroline,

Are you running the python version? I have no idea why MAFFT is taking long on your side, it is usually much faster for large dataset.

[Caroline Tochetto]

Hi :)

Ok, I'using Python 2.7.17  and  MAFFT v7.471.  Here my MAC configs:

 - 1,7 GHz Quad-Core Intel Core i7

 - 16 GB 2133 MHz LPDDR3

The file I'm trying to run has 556 seq with ~400 nt in length. 

Maybe I'm missing something, dont know, but it takes 10 minutes to run 3%.

Thanks in advance!

[Brejnev Muhire]

Thanks  Caroline,

I am not sure what is the issue with MAFFT on MAC.  I has been running well with the Windows Version of SDT.

I think you should troubleshoot by aligning the sequence with MAFFT out of SDT to see how it performs.