How to align a ITS dataset for more than 3000 sequences?

I’d like to analyse a fungal family. I download more than 3000 ITS sequences from GenBank.
I tried to align them by mafft but performed not well.
Could anyone tell me how to obtain a better alignment by mothur?
Thank you very much.


ITS sequences are not homologous to each other so generating a multiple sequence alignment from them really doesn’t work. I’d suggest using mothur’s pre.cluster instead.