Abstract: With the continuous development of biotechnoglogy and progresses in phylogenetics, researchers now are facing more and more challenges and difficulties in reconstructing phylogenetic trees: 1) species number (or individual number) of the specific taxon of research is always increasing; 2) the number of taxonomical characters (for example molecular information) of each species (or individual) is also enlarging. Especially with the efforts of genomesequencing technology, phylogenetic reconstruction based on molecular information requires massive computation. Mathematical methods, computer technologies and other auxiliary means play key roles in enhancing the efficiency and accuracy of phylogenetic reconstruction. Maximum parsimony (MP) is a very important method for phylogenetic reconstruction, and it needs efforts of both biologists and computer scientists to enhance its computational efficiency. In this article, we elaborated the calculation procedure of the MP method in details and analyzed the influences of parameter selection on computational efficiency, in order to help more computer researchers without detailed knowledge of phylogenetics to present better, quicker and more precise solutions to phylogenetic reconstruction in practice. In the meantime, we tried to explain the basic principles and computational logic of the MP method for phylogenetic researchers to push forward continuous improvement and optimization of using maximum parsimony in biology.

Key words: Phylogenetics, phylogenetic reconstruction, algorithm, maximum parsimony, calculation procedure, computational efficiency, optimization