For the analysis, I'm using Geneclass2, Genepop, PGD Spider, Structure, Pophelper (online), Bayescan, Treeview, Arlequin. But i'm facing problem with the PGD Spider as it needs java. Could anybody please let me know the better option to do this analysis? Your help will be gratefully acknowledged.
For your kind information, it's better if the software is free to download.
Cheer!!!!
I'm using Macintosh and I've experienced the same problem with Java environment when using HaploView program.
To launch the program I use the Terminal of the computer by writing the following:
cd ~/Documents/Haploview
java -jar Haplo*.jar
I hope this could be helpful,
Endika
Dear Mr. Khalil,
Just to complete the answer of Mr. Prieto, make sure your java is installed on your system.
What is your Operating System?
To do this verification in GNU-Linux Debian based systems, you can use the command: "java -version" (No quotes). If Java has not been installed, use the command as super-user: "sudo apt-get install openjdk7-jdk" (Java Development Kit) or "sudo apt-get install openjdk7-jre" (Java Runtime Enviroment) and then check that it was installed using the "java -version" command on Terminal.
After installing, the command of Mr. Prieto can work perfectly.
The PGD Spider program is a useful tool for converting files to different formats used in population genetics/genomic.
Report if the problem has been solved.
Regards,
João P. G. Viana
PGD is worth the effort to get it running. I ran into issues installing it on Mac OSX El Capitan and ended up installing it on a Windows machine. The newer Mac OSs make the installation of Java a bit tricky. If you have to install it on a Mac, you'll find some helpful tips here: http://osxdaily.com/2015/10/17/how-to-install-java-in-os-x-el-capitan/
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