The program of misa.pl is a typical program for the identification and localization of simple repeat sequences (SSRs), which can be downloaded from the public website (https://webblast.ipk-gatersleben.de/misa/). However, it can only detect the SSR of one species or one file at a time. Therefore, we have modified and updated this program so that it can batch detect SSRs in multiple species at a time, and we named this program as Batch_SSR_Finder. Anyone engaged in scientific research can download and free use or edit this program from the following links.
>Run program: perl Batch_SSR_Finder.pl -i all_species_dir -o all_species_dir.out
>Program name: Batch_SSR_Finder.pl
>Configure file: The configure file is required named “config.txt” in the folder, which
can be used to specify SSR detection parameters.
>-i (Input file): all_species_dir
The input file is a folder that can hold fasta sequence files of any species, and the number of species is unlimited.
>-o (Output file): all_species_dir.out
The output file is also a folder that contains the output SSR results. There are three result files for each species, *.misa, *.statistics, and *.summary.xls files. The first two files are basic SSR detection result files, which are similar to the results of misa.pl. The *.summary.xls file extracts the key information from the above results. In addition, there is a *.statistics.xls file in the output results folder, which is the SSR statistical result information of all species.