PAUP, Bootstrap and Heuristic searches

James O. McInerney J.McInerney at nhm.ac.uk
Tue Jun 4 03:11:08 EST 1996

Bunny Lover wrote:
> Hello,
> Can any post or point me to where I can learn about bootstrap
> and Heuristic searches using PAUP(on a MAc)>
> I've done the searches already(with a matrix of 0,1 characters)
> but I don't really know(and want to) what the algorhythym's
> do. Essentially Iw ant to learn about how these kinds of
> searches make a tree, etc.
> Thanks a bunch
> Scott


The best thing to do is to get your hands on a copy of 'Molecular 
Systematics" 2nd edition.  It is edited by David Hillis among others.  
There is a chapter called Phylogeny Reconstruction (Chapter 11??) that 
is written by David Swofford (among others).  He is the Author of PAUP.  
The chapter unquestionably is the best piece of literature in press 
today that explains anything and everything about all aspects of 
molecular evolution (including the questions you are posing here).

The paup manual should also help you (or even the manual for MacClade).

Dr. James O. McInerney Ph.D.        Phone/Voicemail: +44 171 938 9247
Senior Scientific Officer,          email:j.mcinerney at nhm.ac.uk
The Natural History Museum,         
Cromwell Road,
London SW7 5BD
UK                                  Gan teanga gan tir.

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