An optimization approach and its application to compare DNA sequences

• We find the optimal weighted distance measures by using linear programming.
• The approach can successfully cluster species at different levels.
• Compared with the ClustalW method, we find ours is better.

Studying the evolutionary relationship between biological sequences has become one of the main tasks in bioinformatics research by means of comparing and analyzing the gene sequence. Many valid methods have been applied to the DNA sequence alignment. In this paper, we propose a novel comparing method based on the Lempel–Ziv (LZ) complexity to compare biological sequences. Moreover, we introduce a new distance measure and make use of the corresponding similarity matrix to construct phylogenic tree without multiple sequence alignment. Further, we construct phylogenic tree for 24 species of Eutherian mammals and 48 countries of Hepatitis E virus (HEV) by an optimization approach. The results indicate that this new method improves the efficiency of sequence comparison and successfully construct phylogenies.