The Construction Of A Phylogenetic Tree Based On DNA Barcode

In recent decades, with the rapid development of molecular biology, thephylogenetic analysis also gradually became into the molecular level, and formed acomplete set of the theory and method which used biological DNA genetic sequencesor protein sequences as the main content of the phylogenetic analysis. Theconstruction of the phylogenetic tree is the widely used research methods of thephylogenetic analysis.How to construct the efficient and accurate phylogenetic tree bymaking the most of the DNA genetic sequence has great significance for thephylogenetic analysis. The construction of the phylogenetic tree includes three steps:1) the molecular sequences or characteristics analysis;2) the construction of thephylogenetic tree;3) the assessment of the phylogenetic tree. The paper carried outthe following three aspects of the research which is around the process of theconstruction of the phylogenetic tree:(1) the feature extraction based on of DNA barcodeThere is no recognized way that construct the phylogenetic tree which used DNAcomplete genome sequence. Now the most methods of the phylogenetic tree are basedon the sequence alignment. And the abnormal formation of DNA sequence caused bythe genetic mutation or alien species invasion and so on, is likely to have a significantimpact of the phylogenetic tree. Because of the above two problems, the way of theconstruction of the phylogenetic tree base on DNA barcode is proposed in the paper.This method has the following advantages:1) used the DNA complete genomesequence;2) didn’t need to the sequence alignment;3) there was no parameters;4)reduced the influence of the genetic mutation and alien species invasion to theconstruction of the phylogenetic tree;5) effective recognition.(2) The improved algorithm of neighbor-joining methodThe paper has carried on the detailed analysis of the neighbor-joining method,and proposed the improved algorithm of the neighbor-joining method. Because theneighbor-joining method has the following two aspects:1) when update the distancematrix in the process of using the neighbor-joining method, every time the notweighed and average distance formula was adopted to estimate the distance betweenthe merged new classification unit and the others, which leads to lacking of the accuracy of neighbor-joining method;2) the distance matrix used to construct thephylogenetic tree in this paper was got through the way which construct thephylogenetic tree based on the DNA barcode in the chapter three in this paper, whichwas nonadditive. So the paper has proposed the improved algorithm of theneighbor-joining method, which mainly used the introduction of the weight formed byvariance and covariance to make the distance estimation, that made the estimate valueof the distance more accurate, and made the application scope of the neighbor-joiningmethod more widely.(3) building an experiment platform of the phylogenetic treeFinally, this paper also built a simple experiment platform of the phylogenetic tree,in order to the conveniention of the construction of the phylogenetic tree. Theexperiement platform mainly includes the neighbor-joining method, the improvedalgorithm, and drawing programe.