MISHIMA

Introduction

MISHIMA is a program for multiple DNA sequence alignment. It takes input in FASTA format and outputs the alignment in MISHIMA or CLUSTALW format.

The idea of this program is to use heuristic to quickly find similarities shared by multiple sequences. Those similarities are then used to split the input sequences into fragments which are aligned separately. After that the partial alignments are assembled back together for complete alignment.

You can try MISHIMA online alignment server:

• MISHIMA server at NIG
• MISHIMA server at kirr.homeunix.org (development version)

You can also download the program to use locally.