phylogenetic trees

Jeroen Coppieters jecop at gengenp.rug.ac.be
Thu Mar 3 04:32:07 EST 1994


On Wed, 2 Mar 1994 Glenn.Brooke at dl.ac.uk 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,
> 
> Glenn Brooke, Ph.D.
> Pioneer Hi-Bred International, Inc.
> brookerg at phibred.com
> 
The program ClustalV (Higgins and Sharp) runs on PC,UNIX,VAX and Mac 
(although not very Mac-like). It can create multiple alignments and uses
the Neighbor Joining method of Saitou and Nei (1987) to create trees.
Only it has no feature to display the resulting tree graphically.
It has the possiblility of writing out the results in a number of formats 
that can be used as input for other programs (like PHYLIP) 
You can ftp the program from ftp at embl-heidelberg.de
and possibly from other places as well.

Jeroen

Ref

Higgins, D.G. and Sharp, P.M. (1989)  Fast and sensitive multiple 
sequence alignments on a microcomputer.  CABIOS 5, 151-153.
Saitou, N. and Nei, M. (1987)  The neighbor-joining method: a new 
method for reconstructing phylogenetic trees.  Mol.Biol.Evol. 4, 
406-425.

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