Mike the Mad Biologist

125 taxa. This analysis is never going to end (stupid GTR models):


I’m getting annoyed….

Update: It took five days to run this thing. And, yes, that was after using ModelTest.

By the way, if you have no idea what I’m talking about, here’s a post (without technical jargon) on likelihood and phylogenetics to introduce you to the basics.


  1. #1 Alex
    September 5, 2007

    I don’t want to be the bearer of bad news, but you’ll probably want to re-do your analysis with several addition sequence replicates- having a single rep, especially with so many taxa, could produce a tree that’s just an artifact of how the taxa were ordered in your matrix.

    Alternately, you could join the civilized world and use MrBayes.

  2. #2 stogoe
    September 5, 2007

    I don’t know if I envy the child who has become “Angry Baby”. I guess on the bright side, his internet fad-dom will most likely have passed on long before he is told about it.

    Off topic, sorry.

  3. #3 Sandra Porter
    September 5, 2007

    What are you running? The screen shot looks like a really old version of something like MacClade on OS 9.

    Maybe you want to look at something newer? Beast is supposed to be really good.

  4. #4 sbotond
    September 14, 2007

    It can be worse. Try some codon models 😀

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