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Re: MacClade vs. PAUP

What does it mean when MacClade (through human manipulation)
comes up with a tree that is two steps shorter than the best one
PAUP can produce?

Apart from the settings... stupid question, but... have you restricted the PAUP* analysis to, say, a certain number of replications because otherwise the computer would be occupied for the next 20 or 30 hours? I almost always limit my analyses, and my matrix isn't all that big (though full of question marks). When I limit the wrong way, I don't always get any of the shortest trees.