Is there a tool to calculate sequence similarity of sequences in a MSA?
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3.5 years ago
DNAngel ▴ 240

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.

alignment DNA • 4.9k views
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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).