I am trying to learn what exactly MAFFT does to align sequences, but i am currently having a hard time to understand it.
I have read its papers and references.
Anyone knows of some kind of tutorial or review for it?
I am researching the FFT-NS-i and E-INS-i algorithms.
Currently, i am trying to understand what are the 6-tuples parameters. I guess the 6-tuples are the weight, volume and charge, compared in pairs of sequences. Is that right?
Thanks in advance
Just in case someone is interested:
Well, i just found out that the 6-tuples are actually a compression of the 20 [aminoacid] alphabet.
Katoh et al., haven't described why they chose the k-mer 6.
Still researching it. I will appreciate any help.
I'm finding much of the information already.
Still some things to go.
In case anyone have interest in this, i can offer help. And i still can use a hand.
End of edits.
Thanks for the answer.
I did read their site and their references. I managed to understand how the FFT-NS-1 and FFT-NS-2 work.
I still have somethings to figure out about FFT-NS-i, and i couldn't get most of E-INS-i (i didn't even found out what the "E" means).
The explanation is spread over many articles, and think some stuff isn't even explained anywhere.