ISO Alignment and Phylogenetic Tree Software

Francois Jeanmougin pingouin at chouchen.u-strasbg.fr
Tue Jan 6 03:06:23 EST 1998

	[posted and mailed]

In article <Pine.GSO.3.94.980105103644.19793B-100000 at morpheus.cis.yale.edu>,
	Emmanuel Skoufos <skoufs at pantheon.yale.edu> writes:

> Dear Bionetters:
> I am looking for a *single* software package (shareware or commercial
> product at a reasonable cost - < $ 500) that runs on Wintel platforms and
> does the following things:
> -Aligns multiple DNA and protein sequences 
> *and* 
> -Builds phylogenetic trees based on the alignments.
> Optimally, cutting and pasting of the sequences is allowed and the tree
> building is an easily executed option on the command menu/tool bar.
> I tried several packages that either did not allow tree construction
> (DNASIS, Prophet) or the user interface was inpractically complicated
> (PHYLIP).  I know that there are a few programs for Macs (including the
> DNASIS version for the Mac) that can do this. 
> If you have any products in mind for a PC, or if any of the products you
> are using does the trick, please let me know.

	Well, for sure, you can try ClustalX, which is free (well, we accept
your $500 grant anyway if you don't know what to do with it ;-).

	It performs multiple alignment of protein or DNA (using a 
transversion/transition matrix if needed or any matrix you would
like to use). It also builds simple phylogenetic trees (but I recommand
you try Phylip ALSO if you need important tree analysis).

	Everything is driven by pull down menus. You can cut and paste
sequences to change the order or to make a hand-driven ordering alignment.

	This software should fit your needs, hopefully. You can get the
last version and doc at :

	Also, for an overview of the programme, just have a look at:

Nucleic Acids Research
Volume 25, Issue 24, Dec 15 1997 (hey! That was my birthday ;-).
The CLUSTAL_X windows interface: flexible strategies for multiple
sequence alignment aided by quality analysis tools
Julie D. Thompson, Toby J. Gibson, Frédéric Plewniak, François Jeanmougin 
and Desmond G. Higgins
pp. 4876-4882

	And please let me know if everything works well at your site.

François Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France

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