Sequence Similarity Of Protein Alignment

Question

[Bjoernsen]

Hi, I would like to calculate the sequence similarity of all protein sequences of a MSA using e.g. JTT, ... The result should be an NxN matrix (N = number of sequences in the alignment).

I there a tool that I can use? I tried BioEdit and 'phylip protdist', but I get an identity matrix and a distance matrix, respectively.

[Neilfws]

Does setting the protdist distance model to "similarity table" give you something close to what you want?

[Bjoernsen]

Thank you, I did not see this setting.

Answer 1

[Niek De Klein]

Doesn't the alignment program already give the sequence similarity? I just tested clustalW and that one does.