This tool is based on EMBOSS command fprotdist that is a wrapper command for command protdist of the PHYLIP package.
Protein distance algorithm computes a distance measure for aligned protein sequences, using maximum likelihood estimates based on the Dayhoff PAM matrix, the JTT matrix model, the PBM model, Kimura's 1983 approximation to these, or a model based on the genetic code plus a constraint on changing to a different category of amino acid. The distances can also be corrected for gamma-distributed and gamma-plus-invariant-sites-distributed rates of change in different sites. Rates of evolution can vary among sites in a prespecified way, and also according to a Hidden Markov model. The program can also make a table of percentage similarity among sequences. The distance matrix can be used as an input for tool: Phylogenies from distance matrix by N-J or UPGMA method.
For more details, please check the manual page of fprotdist command.
Input is a protein multiple sequence alignment.
Output is a text file containing the distance matrix.