Strengths and weaknesses of parsimony and distance methods , used in the PHYLIP 3 . 6 software package

Cytochrome c is an electron-transport protein that has been studied and described in a great detail, as well as has been used in a variety of studies for other purposes. It is a soluble mitochondrial matrix spherical (diameter = 34 A) protein that is associated to the inner mitochondrial membrane and has the function of transferring electrons between respiratory chains III and IV. Cytochrome c is present in almost all organisms that have mitochondrial respiratory chains, including plants, animals and microorganisms (Stryer 1988). The sequence for cytochrome c has been determined for a large number of organisms (more than 70) and is usually 104 amino acid residues long. The consensus pattern for its family is Cys-X-X-Cys-His (or C-{CPWHF}-{CPWR}C-H-{CFYW}). It consists of one polypeptide chain and has covalently attached heme group by means thioether bonds to two conserved cysteine residues. “The iron atom is bonded to the sulfur atom of the methionine residue and to the nitrogen atom of the histidine residue,” (Stryer 1988) both of which have been conserved in all species. The sequence has 26 completely conserved residues, including the cysteine and histidine residues mentioned above. A large number of studies on the cytochrome family evolution have been done. The purpose of this paper will be to discuss some strengths and weaknesses of the parsimony and distance methods, examined by means of phylogenetic analysis of the cytochrome c family, using the PHYLIP software package, provided by Joseph Felsenstein.