Is there a tool to calculate sequence similarity of sequences in a MSA?

Question

[DNAngel]

I have many multiple sequence alignments containing protein-coding genes aligned by codons and I want to generate pairwise similarity tables between each pair of sequences. I know Geneious used to do this but I no longer have it on trial nor can I afford to buy it.

[Joe]

This previous thread may help:

Make matrix of protein pairwise identities/similarities from multiple protein sequences

[GenoMax]

I don't know what the Geneious output looked like but you could also look at Plotting sequence similarity/identity of a multiple sequence alignment (and infoalign program from EMBOSS).