Sometimes, Phylogenetic Analysis Takes a Really Long Time

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.

This entry was posted in Bioinformatics, Evolution, Likelihood, Statistics. Bookmark the permalink.

4 Responses to Sometimes, Phylogenetic Analysis Takes a Really Long Time

  1. Alex says:

    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. stogoe says:

    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. 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. sbotond says:

    It can be worse. Try some codon models 😀

Comments are closed.