Download everything in one click for Windows and Mac, and for everything else use the Linux install script.
Click here, download (and unzip) the file (v1.3a), then double-click on 'phyloGenerator.exe'. Make sure you save the program somewhere you have permission to write data, so not just in "C:\", as otherwise the program will crash (check the FAQ).
Using the BEAST options requires you to have Java installed. If in doubt, or if this section of the program crashes re-install Java and then read the FAQ entry on BEAST crashes.
Some browsers on Windows computers (not on anything else!) are concerned the file is a virus; it's not. If the file is blocked, go to the download section within your browser and unblock it. The button varies by browser and computer; on Chrome I had to click 'hurt me plenty' when a dialogue box appeared. The way I've bundled Python and various phylogenetic programs into pG apparently looks like a virus, sorry!
Some users have also reported that pG, and some of the programs it uses internally, are being flagged as dangerous by anti-virus programs. If this is happening to you, it will stop the program working - go into your anti-virus software and allow pG and all the programs it calls to run.
Have a quick look through the 'README.txt' file, and check out the 'Demos' folder for examples of how to get it working from the command prompt.
Tested on Windows 7 and 8. If you find the program crashes/suddenly exits when running BEAST, please check the FAQ.
Using the BEAST options requires you to have Java installed, and what ships with MacOS is no longer sufficient to run BEAST in phyloGenerator. If this section of the program crashes re-install Java and then read the FAQ entry on BEAST crashes.
Should you encounter errors, please report them. Note there was a bug that may have affected some BEAST runs in earlier versions (1.1a and earlier) of the program (see here); if you are in any way concerned about your analyses please contact me with a DropBox link to your output.
Click here, download (and unzip) the file (v1.3a), then run './phyloGenerator.app/Contents/MacOS/phyloGenerator' from Terminal when in the directory you unzipped it all into.
Using the BEAST options requires you to have Java installed. If in doubt, or if this section of the program crashes re-install Java and then read the FAQ entry on BEAST crashes.
Have a quick look through the 'README.txt' file for more details on how this works, and check out the 'Demos' folder for examples of how to get it working from the command prompt.
Tested on Mac OS 10.10 (Yosemite)
Should you encounter errors, please report them. Note there was a bug that may have affected some BEAST runs in earlier versions (1.1a and earlier) of the program (see here); if you are in any way concerned about your analyses please contact me with a DropBox link to your output.
Please register for the phyloGenerator mailing list. This way you can get help easily, I can keep you informed of updates, and you can make feature requests more easily.
Download the source code from GitHub here, and (from Terminal) run the linuxSsetup.py script (something like python linuxSetup.py. If you don't have python installed, try sudo apt-get install python. Note there was a bug that may have affected some BEAST runs in earlier versions (1.1a and earlier) of the program (see here); if you are in any way concerned about your analyses please contact me with a DropBox link to your output.
Please register for the phyloGenerator mailing list. This way you can get help easily, I can keep you informed of updates, and you can make feature requests more easily.
This will not work first time! The script will tell you what things are yet to be installed, and give you a web link to follow that will have the download you need, or recommend something to type into your console to set that component up for you.
The script is setting up symbolic links for the programs you're downloading in a folder called 'requires'. This means that moving the programs once you've set up phyloGenerator will cause phyloGenerator not to work. So put those programmes somewhere safe, like inside your phyloGenerator folder.
When running the setup script, make sure you tell it where these programs are by supplying their paths as arguments. You can specify as many paths as you like. Make sure you specifically tell it where your BEAST folder is - something like: python setupLinux.py /work/will/phyloGenerator/ /work/will/phyloGenerator/BEASTv1.7.1.
The script should be able to auto-detect the names of the programs it's looking for in each of your folders. This could go wrong - if it does, change the name of the program to that shown in the next column. For example, ideally Clustal-Omega would be called 'clustalo', and renaming the program to that should solve any problems.
If the name is right, but the script still isn't working, make sure the program's permissions are set up right to let your computer execute it. Just type something like chmod 777 NAMEOFPROGRAM and phyloGenerator will be able to execute the program.
You don't necessarily need all of these programs (...only the ones you're going to use...) but the complete list is below. Once you've compiled them, put all of them in safe folder and run setupLinux.py with that folder as an argument (see the column to the left).