Amino acids maximum parsimony

Fig. 5. Phylogenetic analysis of NRF family amino acid sequences. The amino acid sequences of known or predicted members of the NRF family in zebrafish and pufferfish were obtained from the GenBank or genome databases and aligned with the human NRF family sequences. The tree was inferred using maximum parsimony within PAUP 4b 10. The results illustrate the conservation of NRF proteins in mammals and fish as well as the additional diversity in NRF3 forms present in pufferfish. Danio rerio (Dr), Takifugu (Fugu) rubripes (Fr), Homo sapiens (Hs).

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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