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Re: Need help doing phylogenetic analyses

>Thanks to everyone who responded, but I still have problems.  Both Adam
>Yates and Gareth Dyke suggested I pull down the "trees" menu and go to the
>"describe trees" option, then click on the "list of apomorphies" button.
>The only problem being I don't have a "trees" menu, I only have "file",
>"edit", "window" and "help".  If it helps, I have PAUP* 4.0b4a.  Further
>information would be helpful.  Others suggested I use MacClade.  Can I use
>this program with Windows, or just on a Macintosh?  Thanks again for any
>Mickey Mortimer

The command to get an apomorphy list is in the dialogue box used when you
ask PAUP to describe a tree.  The default settings in this box simply give
you the standard stats (length, CI, RI, etc.), but you can check off the
box for "apomorphy list," and PAUP will list the apomorphies below the tree.

THe default setting for apomorphies, I believe, is ACCTRANS.  You will have
to specifically ask PAUP to switch over to DELTRANS and get a second list.
In versions of PAUP 4, this is under the "parsimony settings" submenu; in
earlier versions, it was somewhere else (I think under the "data" menu,
"character optimization" submenu).  I'm doing this from memory - my hard
drive croaked last week, and I don't have access to PAUP at the moment, so
the actual names of these submenus may be different.

MacClade is a great program, but it has limitations for getting apomorphy
lists, especially when there are polytomies in the tree.  You should always
use a fully-resolved tree to get apomorphies, and should always look at the
reasons for why ACCTRANS and DELTRANS optimizations are different - very
often, this will boil down to missing data and/or different resolutions of
polytomies on the tree.

A draft of the PAUP user's manual can be obtained from the PAUP web site,
which should be accessable through www.sinauer.com.