drawing trees

[Jennifer Steinbachs]

Use your favourite alignment program...
Put your aligned sequences into PHYLIP format
Run the appropriate phylip program...
    distance-based methods:
	protdist (for proteins)
	dnadist (for dna)
    parsimony
	protpars
	dnapars
    likelihood
	dnaml or dnamlk
	protml

See the phylip website
for more info (http://evolution.genetics.washington.edu/phylip.html).

If you aren't certain of the differences between the different
tree-building algorithms, you should get your hands on Nei and Kumar 2000
Molecular Evolution and Phylogenetics ISBN 0-19-513585-7.  The other good
reference for phylogenetics is Hillis et al 1996 Molecular Systematics
ISBN 0-87893-282-8 Chapter 11.

-jennifer



On Mon, 27 Aug 2001, Gene Cutler wrote:

 >Hello, all.  I have a question about phylogenetic-type trees for
 >sequences.  I haven't quite figured out how to do this using
 >emboss/phylip.  This is how I have been doing this with gcg:
 >
 >perform multiple sequence alignment (generally hmmalign or clustalw)
 >convert file to msf format if not already (e.g., sreformat from hmmer package)
 >run gcg program distances on the msf file
 >run gcg program growtree on the distances file
 >end up with a postscript file
 >
 >How would I do this with PHYLIP instead?
 >
 >Thanks.
 >
 >


-----------------------------------
J. Steinbachs, Ph.D.
Computational Biologist
http://compbiology.org
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