Abstract: Multiple sequence alignment is an important part of bioinformatics research, which is the basis to solve the problems of species evolution relationship and genome sequence analysis. Multiple sequence alignment algorithms have high specificity and different algorithms are suitable for different research environments. At present, the commonly used multiple sequence alignment software is based on the assembly of multiple sub-algorithms under the guidance of bioinformatics theory. However, the existing research mainly focuses on the optimization of specific steps of specific algorithms, and the lack of algorithm framework research with high abstraction of domain level leads to the complexity and redundancy of multiple sequence alignment algorithms. According to the idea of generative programming and software reuse, the features of 
multiple sequence alignment algorithm (MSAA) are analyzed and modeled, and the corresponding generic algorithm components are designed and the interaction among these components is described. Further, PAR platform is used to formally build up the MSAA component library. The work improves the reliability and assembly flexibility of assembling algorithms and facilitates the maintenance and optimization of researchers.

Key words: multiple sequences alignment algorithm;feature model, generative programming;algorithm component;PAR platform