title: Determination of optimal parameters of MAFFT program based on BAliBASE3.0 database.
abstract: BACKGROUND
  Multiple sequence alignment (MSA) is one of the most important research contents in bioinformatics. A number of MSA programs have emerged. The accuracy of MSA programs highly depends on the parameters setting, mainly including gap open penalties (GOP), gap extension penalties (GEP) and substitution matrix (SM). This research tries to obtain the optimal GOP, GEP and SM rather than MAFFT default parameters.
  
  
  RESULTS
  The paper discusses the MAFFT program benchmarked on BAliBASE3.0 database, and the optimal parameters of MAFFT program are obtained, which are better than the default parameters of CLUSTALW and MAFFT program.
  
  
  CONCLUSIONS
  The optimal parameters can improve the results of multiple sequence alignment, which is feasible and efficient.
authors.affiliation: School of Information Science Technology, Hainan Normal University, Haikou, 571158 HaiNan China.
authors.forename: HaiXia
authors.initials: H
authors.lastname: Long
authors.affiliation: School of Mathematics and Statistics, Hainan Normal University, Haikou, 571158 HaiNan China.
authors.forename: ManZhi
authors.initials: M
authors.lastname: Li
authors.affiliation: School of Information Science Technology, Hainan Normal University, Haikou, 571158 HaiNan China.
authors.forename: HaiYan
authors.initials: H
authors.lastname: Fu
keywords: Default parameters; Gap extension penalties; Gap open penalties; MAFFT program; Multiple sequence alignment; Substitution matrix