探讨了核糖体小亚基二级结构对真菌系统发育分析的影响。对用不同方法构建的系统发育树进行比较，结果表明结合二级结构信息的分析方法较传统方法产生了更为合理的拓扑结构。二级结构信息除用于优化序列比对外，还需整合到核酸替代模型中；恰当的序列比对方法、进化模型和建树运算法则有助于更加准确地揭示类群之间的亲缘关系。

Different methods using rRNA secondary structure to assist phylogenetic analyses have been recently developed. In order to evaluate the structure information on accuracy of phylogenetic tree topology, comparisons of these methods were performed. Our results showed significant superiority of phylogenetic analyses incorporating secondary structure over the pure traditional approaches. When the three major factors, alignment method, evolutionary model and tree search algorithm, were considered simultaneously in phylogenetic analyses, the implementation of structure information in alignment and substitution model produced a noticeable positive effect on topological accuracy.