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phylogenetic trees

David R. Maddison dmaddsn at ccit.arizona.edu
Thu Mar 3 12:53:13 EST 1994

In article <CM23E9.109 at phibred.com>, Glenn Brooke, Ph.D.
<brookerg at phibred.com> wrote:

> 	Aside from the program suite PHYLIP, does anyone have suggestions
> for software to take short (<150) nucleotide sequences and create
> phylogenetic trees?  Preferred platform in Macintosh, but we have
> unix and PCs available.  Thanks in advance,

Some of the software you might consider on the Mac is:

* PAUP (parsimony & Lake's Invariants, diverse array of features, by far
the most comprehensive of parsimony-based tree inference programs)
   Author: David Swofford
   Contact: paup at onyx.si.edu.  (I think distribution is still in limbo)

* MacClade (parsimony based, intended less for tree inference and more
for examining character evolution, manipulating trees, entering data, 
producing graphics, etc.)
   Authors: Wayne Maddison & David Maddison
   Contact: biology at world.std.com (Sinauer Associates)

On the PC side I would consider looking at
  MEGA (various distance methods, parsimony)
  HENNIG86 (parsimony based; very fast but fewer features)
  CLADOS (parsimony based, more for looking at character evolution and
  NTSYS (various distance methods)
  COMPONENT (various important tree analyses; not for tree inference)

There's more but these are the more widely distributed ones that come
to mind at the moment.  Check out the PHYLIP documentation for more

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