Amino acids maximum likelihood

Fig. 6.1 Schematic illustration of the observed spatial distributions of hydrogen bond partners for several amino acids [13, 16], Darker shading indicates an increased likelihood of finding a hydrogen bond partner at a particular position. Most groups have maximum likelihood of having their partner located in...

The third (default) method uses a table of empirically observed transitions between amino acids (the Dayhoff PAM 001 matrix). The character-based analysis of sequence data can be initiated via the appropriate executable file (e.g. DnaPars, DnaML or ProtPars). PHYLIP comprises DnaPars and DnaML to estimate phylogenetic relationships by the parsimony method and the maximum likelihood methods from nucleotide sequences respectively. ProtPars is the parsimony program for protein sequences. 

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