In　this　paper,　the　neural　network　of　self-organizing　map　is　used　to　overcome　the　tie　tree　drawback,　which　is　a　serious　problem　in　traditional　phylogenetic　tree　reconstruction,　and　improve　the　preciseness　of　phylogenetic　tree.　The　multifurcating　tree　is　also　reconstructed　to　replace　the　role　of　traditional　binary　tree,　so　that　the　system　evolution　be　displayed　more　precisely.　By　giving　proper　parameters,　the　arrangement　and　sequence　cluster　can　be　optimized.　The　experiments　indicate　that　this　method　is　effective.