GMATA software for Genomic SSR marker Wiki

**Citing **
Wang X, Wang L (2016) GMATA: an integrated software package for genome-scale SSR mining, marker development and viewing. Frontiers in Plant Science 7 (1350). doi:10.3389/fpls.2016.01350
Published article: http://journal.frontiersin.org/article/10.3389/fpls.2016.01350/full

Instructions for software GMATA
---- a complete solution from genomic sequence to SSR marker development, and statistics, graphic plotting, Marker e-PCR, marker transferability, SSR and marker graphic displaying with other generic feature....

Latest version V2.3
20210806
This version works for any sequence in fastq or fasta format from Illumina, PacBio and more . Please download the latest version v2.3 in .zip file called "GMATA-master_v2.3". For more details on this version, please see Github at https://github.com/XuewenWangUGA/GMATA

Previous version in v2.1
Previous old version v2.01 is not available online from Feb 3rd 2016. Please use the latest version of GMATA. All results produced previous version of GMATA will be compatible with newest version, so you can use your previous results in the new version. The graph GUI and manual may display the old version number but it is working well with V2.1

**Installation **

1. download all files
2. make a new directory such as "GMATAv2.3" or any name you like
3. use software 7zip or zip to un-compress binxx.zip to the same directory GMATA
4. download and copy GMATA.jar to the same directory GMATA
5. go to directory GMATA, click GMATA.jar to start the using or follow manual for command line usage
6. for testing, download the test data "data.zip". some pre-run results from GMATA are also provided in test data.

example graph output:
Statistical graph output results for whole genome sequence of four crop species: rice (O.sativa), foxtail millet (Setaria italica), corn (Z. mays), B. distachyon were provided for your convenience. You can unzip the download zip file, and then unzip you will find the beautiful graphs (genome version information was included in the name of each graph).

If you want to try the test data, you can download the data.zip and unzip the file. Then when you run the software, you can use the test data. The test data contains more than 3000 DNA sequences , which take less than 1 second to get analyzed in software GMATA.

Other software needed:
The program is provided as source code. Therefore additional software may require to provide running environment.

For Windows users:
You need to install the lastest "Perl 5 " version 5.x.xx , noting NOT perl 6.
and install R 2 or R 3.0 before use GMATA for your Windows system.
After install Perl 5 , you want to test installation is good or not. You can go to right click "Windows" icon in the far left bottom to choose "run" and then type "perl". If you can see a welcome message of perl, it means that you are successfully installed Perl. Otherwise, you have to set Perl to environment variable in Windows. alternative you can double click Perl icon in your desktop to make sure it is correctly installed.
After installing R, you want to go to right click "windows" icon in the far left bottom to choose "run" and then type "R". If you can see a welcome message of R, it means that you are successfully installed R. Otherwise, you have to set R to environment variable in Windows.

For Linux and Mac users:
Linux and Mac OS already have Perl installed , so you may not need to install any software of computing language. For the other dependent packages, please refer to manual of GMATA.

I am updating the manual and hopefully a new version will be available soon with more details.

If you have any question, please do not hesitate to contact with me or get the section of "Discussion" at sourceforge.net.

**Contact **
Dr Xuewen Wang
email: xwwang@ymail.com