automated phylogenetics for brave

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I'm really sorry if you're having problems that none of the above can help you with. Please, please, please do get in contact if you're having trouble getting the program to work. I will do everything I can to help you, but I can help you best if you follow the checklist below (in order, I guess):

  1. Read this website, the original pG paper, and search the mailing list
    Most questions are answered somewhere on one of those three things.

  2. Simplify your problem to the bare minimum
    By working with the simplest example that generates the problem, you make it easier for me to isolate the problem. Please find the closest thing you can to a minimal, complete, verifiable example - 9/10 this process will help you find the solution anyway.

  3. Give me what I need to solve your problem
    I need to know:
    • The entire error message (please don't 'give me the gist'!) and all preceeding output
    • Your input, i.e., the parameter file, your reference sequences, and the species list. I promise never to share it with anyone.
    • What operating system you're using and its version (e.g., Windows 8.1, Mac OS 10.10.1)
  4. Use the mailing list
    I get a lot of emails about pG, and many of them are about the same thing. I set up the mailing list to help with this.

I like talking to people, and I like helping people. If you get in touch with me, I promise I will do everything I can to help you. Don't be put off by a four-point list of things to do; I'm not an ogre, and I will buy you a beer if you get in touch...