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Re: PAUP and pteros



I think I can't answer this one without disclosing that I am the one who got
the matrix. I have to thank again for the trust -- the matrix is
unpublished.

> >> Originally I planned to run your matrix without the problematic
> characters and the obvious babies through PAUP*... but it turns out
> that this would be a huge amount of work. It's better if you do this.>>
>
> In my experience, running PAUP is as easy as pressing a button.

You overlooked the "without the problematic characters" part. This would
mean to first disentangle the partially interdependent characters. That
would take a lot of time. States 159(0), 160(0) and 161(0), for example, are
the same thing, but 159(1), 160(1) and 161(1) are three different things.

And then don't forget the ordering.

> To that critic: you blinked.

I've seen THE BIG ONE, but I forgot who it was who never blinked...

> I hope you weren't afraid of what you might find.

Look... university takes up some time, even when there are no exams
(there'll be one on November 19th, then sometime in December, and on
November 3rd I'm supposed to give a little talk on phylogenetic
nomenclature, which nobody in the university save me and one other person
have ever heard about. And then I currently get up to 100 e-mails per day!
If it were as simple as removing some characters and/or taxa, I'd have run
it yesterday evening. It just isn't.

> But then what do you do with all those tiny taxa?

Why do you think they are taxa of their own, as opposed to babies of other
taxa?

> I think it's important to send your work to your harshest critics. That
> way you'll know you'll get a good "punch a fist in your face" [to quote
> my critic again]

...mightily out of context...

> if they find something amiss. One other critic, no
> longer on the DML, said he trashed the matrix as soon as he got it.

Considering the current state of the matrix -- not its potential, just its
current state --, this is easily understandable.