Re: smallest pteros

[David Marjanovic <david.marjanovic@gmx.at>]

----- Original Message -----
From: "Mickey Mortimer" <Mickey_Mortimer111@msn.com>
Sent: Friday, October 22, 2004 2:14 AM

> > Warning!!! I don't know about MacClade, but PAUP* automatically
interprets
> > "-" as a gap -- as a deletion in a molecular sequence (respectively as
an
> > insertion in the other taxa). _Never_ put this symbol into a purely
> > morphological data matrix!!! You will get bogus results.
>
> Is that so?  Does PAUP treat a gap as a state that can group taxa
together?

You can choose if PAUP* treats indels as missing data or as a fifth state. I
forgot what the default setting is.

> Because I've been using '-' as 'inapplicable' in my coelurosaur analysis
> this whole time.  Let's see what replacing it with '?' does to the tree.

Don't do that. "Inapplicable" and "unknown" are usually _not_ the same.

There are only two solutions -- either reconfigure all those characters, or
use a program that can actually deal with inapplicable states, such as NONA
or TNT.