Sequence Similarity Of Protein Alignment
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.
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Niek De Klein
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Bjoernsen •
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Bjoernsen •
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Doesn't the alignment program already give the sequence similarity? I just tested clustalW and that one does.
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Does setting the protdist distance model to "similarity table" give you something close to what you want?
Thank you, I did not see this setting.