How trustworthy are the fast MAFFT algorithms (Progressive Methods)? I like using G-INS-i, but now I have to align about 500 sequences and the alignment is extremely slow . I've run the alignment at Galaxy Server, but 15 hours have already passed by and it keeps going.
So, I would like to know if progressive aligments, such as FFT-NS-2, are trustywoth. The alignments are going to be used for phylogenetic analyses.
Thank you in advance!