Is there a tool to calculate sequence similarity of sequences in a MSA?
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.
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This previous thread may help:
Make matrix of protein pairwise identities/similarities from multiple protein sequences
I don't know what the
Geneiousoutput looked like but you could also look at Plotting sequence similarity/identity of a multiple sequence alignment (andinfoalignprogram from EMBOSS).