processing functional genes

I have amino acid sequences of a functional gene in ARB. All are well aligned.In ARB I have calculated the distance matrix and saved in phylip format.
After exporting it, can I use it in Mothur (eg. for rarefaction curves, diversity indices, clustering) as described in the following Tutorial http://www.mothur.org/wiki/Analysis_of_the_aclB_gene_in_a_hot_spring:_a_non-16S_rRNA_gene_example?
Looking forward to your answers.

That tutorial is pretty out of date at this point. I’d suggest looking at the 454 SOP and picking up after you calculate distance matrices (http://www.mothur.org/wiki/454_SOP#Preparing_inputs_for_analysis)