Sequence Similarity Of Protein Alignment
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11.9 years ago
Bjoernsen ▴ 40

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.

msa protein similarity • 3.9k views
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Does setting the protdist distance model to "similarity table" give you something close to what you want?

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Thank you, I did not see this setting.

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11.9 years ago
Niek De Klein ★ 2.6k

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

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