I have aligned a set of sequence with MAFFT. Unfortunately the alignment is not perfect (gap) and
1) I am wondering if I need to filter somehing. Based on that paper :
It's apparently not good to filter. Did you have some experience about that ?
2) I would like to use MEGA 7 (or something else you can recommend) to compute the model that I sould use for maximul likelihood inference.
How can I import MAFFT result to MEGA ? The only thing I see is importing fasta file and align with muscle or clustal