Recent changes to Home

Home modified by Xuewen Wang

Xuewen Wang — Fri, 06 Aug 2021 21:19:06 -0000

--- v8
+++ v9
@@ -3,37 +3,41 @@
 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 statistcs, graphic plotting, Marker e-PCR, marker transferability, SSR and marker graphic displaying with other geneic feature....
+---- 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....

-**Lastest version in v2.1**
-Previous old verion 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 compatbile 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
+**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 "GMATAv21" or any name you like
-3. use software 7zip or zip to un-compress binxx.zip to the same directory GMATAv21
-4. download and copy GMATA.jar to the same directory GMATAv21
+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 tesing, download the test data  "data.zip". some pre-run results from GMATA are also provided in test data. 
+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 covinience. You can unzip the download zip file, and then unzip you will find the beatiful graphes (genome version infomation was included in the name of each graph). 
+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 tes data contains more than 3000 DNA sequences , which take less than 1 second to get analysed in software GMATA.
+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 softwae may require to provide running enviroment.
+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" ico 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 enviroment variable in Windows.  alternative you can double click Perl ico in your desktop to make sure it is correctly installed. 
-After installing R, you want to go to right click "windows" ico 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 enviroment variable in Windows. 
+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 computting language. For the other dependent packages, please refer to manul of GMATA. 
+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.

Home modified by Xuewen Wang

Xuewen Wang — Thu, 20 Oct 2016 15:13:50 -0000

--- v7
+++ v8
@@ -6,7 +6,7 @@
 ---- a complete solution from genomic sequence to SSR marker development, and statistcs, graphic plotting, Marker e-PCR, marker transferability, SSR and marker graphic displaying with other geneic feature....

 **Lastest version in v2.1**
-Previous old verion 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 compatbile with newest version, so you can use your previous results in the new version.
+Previous old verion 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 compatbile 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  **

@@ -16,6 +16,9 @@
 4. download and copy GMATA.jar to the same directory GMATAv21
 5. go to directory GMATA, click GMATA.jar to start the using or follow manual for command line usage
 6. for tesing, 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 covinience. You can unzip the download zip file, and then unzip you will find the beatiful graphes (genome version infomation 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 tes data contains more than 3000 DNA sequences , which take less than 1 second to get analysed in software GMATA.

Home modified by Xuewen Wang

Xuewen Wang — Tue, 11 Oct 2016 17:10:47 -0000

--- v6
+++ v7
@@ -11,25 +11,30 @@
 **Installation  **

 1. download all files 
-2. make a new directory such as "GMATAv21"
-3. use software 7zip or zip to un-compress binxx.zip to directory GMATAv21
-4. download and copy GMATA.jar to directory GMATAv21
-5. go to directory GMATA, click GMATA.jar to start the usage or follow manul for command line usage
-6. for tesing, download the test data  "data.zip". A pre-run results from GMATA are also provided in test data. 
+2. make a new directory such as "GMATAv21" or any name you like
+3. use software 7zip or zip to un-compress binxx.zip to the same directory GMATAv21
+4. download and copy GMATA.jar to the same directory GMATAv21
+5. go to directory GMATA, click GMATA.jar to start the using or follow manual for command line usage
+6. for tesing, download the test data  "data.zip". some pre-run results from GMATA are also provided in test data. 

 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 tes data contains more than 3000 DNA sequences , which take less than 1 second to get analysed in software GMATA.

 Other software needed:
-The program is provided as source code. 
+The program is provided as source code.  Therefore additional softwae may require to provide running enviroment.

 >>>>>For Windows users: 
-You need to install the lastest "Perl 5 " version 5.x.xx and install R 2 or R 3.0 before use GMATA for your Windows system. After installing R, you want to go to right click "windows" ico 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 enviroment variable in Windows. 
+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" ico 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 enviroment variable in Windows.  alternative you can double click Perl ico in your desktop to make sure it is correctly installed. 
+After installing R, you want to go to right click "windows" ico 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 enviroment 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. For instruction, please refer to manul of GMATA. I am updating the manul and hopefully a new version  will be available soon with more details.
+Linux and Mac OS already have Perl installed , so you may not need to install any software of computting language. For the other dependent packages, please refer to manul of GMATA. 

-If you have any question, please do not hesitate to contact with me.
+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

Home modified by Xuewen Wang

Xuewen Wang — Wed, 21 Sep 2016 12:47:14 -0000

--- v5
+++ v6
@@ -1,6 +1,6 @@
 **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/abstract
+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 statistcs, graphic plotting, Marker e-PCR, marker transferability, SSR and marker graphic displaying with other geneic feature....

Home modified by Xuewen Wang

Xuewen Wang — Tue, 30 Aug 2016 13:29:06 -0000

--- v4
+++ v5
@@ -1,3 +1,7 @@
+**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/abstract
+
 **Instructions for software GMATA**
 ---- a complete solution from genomic sequence to SSR marker development, and statistcs, graphic plotting, Marker e-PCR, marker transferability, SSR and marker graphic displaying with other geneic feature....

Home modified by Xuewen Wang

Xuewen Wang — Thu, 04 Feb 2016 00:49:06 -0000

--- v3
+++ v4
@@ -1,10 +1,10 @@
-instructions for software GMATA
+**Instructions for software GMATA**
 ---- a complete solution from genomic sequence to SSR marker development, and statistcs, graphic plotting, Marker e-PCR, marker transferability, SSR and marker graphic displaying with other geneic feature....

-Lastest version in v2.1
+**Lastest version in v2.1**
 Previous old verion 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 compatbile with newest version, so you can use your previous results in the new version.

-Instructions for installationof GMATA :
+**Installation  **

 1. download all files 
 2. make a new directory such as "GMATAv21"
@@ -26,7 +26,8 @@
 Linux and Mac OS already have Perl installed , so you may not need to install any software. For instruction, please refer to manul of GMATA. I am updating the manul 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.
-Contact: 
+
+**Contact **
 Dr Xuewen Wang
 email: xwwang@ymail.com

Home modified by Xuewen Wang

Xuewen Wang — Thu, 04 Feb 2016 00:47:28 -0000

--- v2
+++ v3
@@ -1,14 +1,32 @@
 instructions for software GMATA
 ---- a complete solution from genomic sequence to SSR marker development, and statistcs, graphic plotting, Marker e-PCR, marker transferability, SSR and marker graphic displaying with other geneic feature....

+Lastest version in v2.1
+Previous old verion 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 compatbile with newest version, so you can use your previous results in the new version.

 Instructions for installationof GMATA :

 1. download all files 
-2. make a new directory such as "GMATAV201"
-3. use software 7zip to un-compress bin.7z to directory GMATAV201
-4. copy GMATA.jar to directory GMATAV201
-5. click GMATA.jar to start the usage
+2. make a new directory such as "GMATAv21"
+3. use software 7zip or zip to un-compress binxx.zip to directory GMATAv21
+4. download and copy GMATA.jar to directory GMATAv21
+5. go to directory GMATA, click GMATA.jar to start the usage or follow manul for command line usage
+6. for tesing, download the test data  "data.zip". A pre-run results from GMATA are also provided in test data. 

-If you want to try the test data, you can download the data.7z and unzip the file. Then when you run the software, you can use the test data. The tes data contains more than 3000 DNA sequences , which take less than 1 second to get analysed in software GMATA.
+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 tes data contains more than 3000 DNA sequences , which take less than 1 second to get analysed in software GMATA.
+
+Other software needed:
+The program is provided as source code. 
+
+>>>>>For Windows users: 
+You need to install the lastest "Perl 5 " version 5.x.xx and install R 2 or R 3.0 before use GMATA for your Windows system. After installing R, you want to go to right click "windows" ico 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 enviroment 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. For instruction, please refer to manul of GMATA. I am updating the manul 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.
+Contact: 
+Dr Xuewen Wang
+email: xwwang@ymail.com 
+

Home modified by Xuewen Wang

Xuewen Wang — Fri, 08 Jan 2016 20:49:53 -0000

--- v1
+++ v2
@@ -1,8 +1,14 @@
-Welcome to your wiki!
+instructions for software GMATA
+---- a complete solution from genomic sequence to SSR marker development, and statistcs, graphic plotting, Marker e-PCR, marker transferability, SSR and marker graphic displaying with other geneic feature....

-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

-The wiki uses [Markdown](/p/gmata/wiki/markdown_syntax/) syntax.
+Instructions for installationof GMATA :

-[[members limit=20]]
-[[download_button]]
+1. download all files 
+2. make a new directory such as "GMATAV201"
+3. use software 7zip to un-compress bin.7z to directory GMATAV201
+4. copy GMATA.jar to directory GMATAV201
+5. click GMATA.jar to start the usage
+
+
+If you want to try the test data, you can download the data.7z and unzip the file. Then when you run the software, you can use the test data. The tes data contains more than 3000 DNA sequences , which take less than 1 second to get analysed in software GMATA.

Home modified by Xuewen Wang

Xuewen Wang — Fri, 18 Dec 2015 10:45:37 -0000

Welcome to your wiki!

This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

The wiki uses Markdown syntax.

Project Members:

Xuewen Wang (admin)