Posted by Mike on September 5, 2007 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.
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.
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.
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.
It can be worse. Try some codon models 
September 5, 2007
September 5, 2007
September 5, 2007
September 14, 2007