Calculate weighted and unwieghted Unifrac

Question

[chiara.conte91]

Hello there! I am trying to calculate the Unifrac matrix for the 16S rRNA samples I usually do it with Qiime2 but unfortunately, I cannot access to the server I usually work with at the moment.

I aligned the rep seq with MEGA5 and I got a fasta aligned file. I was going to use this but I keep getting the following error: Invalid character encountered in data file that does not allow me to make a phylogenetic tree.

I tried to use phyloseq but it is not supported my R version (that I have just updated)

So my question are: How can I solve these issues? or How can I make a Phylogenetic tree to get the Unifrac?

Thank you very much!!