Although gap penalties affect the results of multiple sequence alignment, it is not clear whether there is difference among results got when using different gap coding method and tree search method. 虽然空位罚分显著地影响多序列比对,但是并不清楚当空位以不同的方法编码和使用不同的重建算法时系统发育分析结果是否存在差异。
There are many algorithms in this area, which are based on objective functions. The objective functions use substitution matrix and gap penalty to score the processes and results of alignment, and judge the results according to the scores of alignment. 现有的很多比对算法都是基于目标函数,目标函数利用替换矩阵和空位罚分对比对过程和结果进行记分,用记分值来判断序列比对结果的好坏。