Hi there,
I have been using mothur to analyse protein sequences (after alignment and distance matrice in Clustal O)-
I was wondering if the Alpha and Beta diversity measurements set it mothur would work also for protein sequences in theory? (it works on the program )
Specifically when using the dist.shared with a Bray-Curstis calculator?
many thanks
kim
In theory it works. There are two problems. The first is a practical, at this point you cannot calculate a sequence-based distance matrix between protein sequences in mothur. You’ll have to use something else for that. The second is theoretical - what cutoff to use. We don’t have a great answer for that. In reality we don’t really have a great answer for 16S (i.e. 0.03), but it works and makes some sense empirically.
Ok cool thanks
Yes distance matrix I used Clustal O and For this specif gene generally we use a o.1 cutoff…so I just built a .shared file 
Would be awesome if in the future Mothur can do more stuff with proteins… I really like this program it is great! 