Julie Knott jknott at MOLBIO.CBS.UMN.EDU
Mon Sep 5 22:48:31 EST 1994

FROM ED at molbio1.uct.ac.zq on 2 Sept 1994

Yes - don't use PileUp...!  Use CLUSTALV: in my experience this is 
better for alignments where what you're trying to align are much the 
same length as each other, AND it gives you a dendrogram in tabular 
form from the initial pairwise alignment scores which you can 
use to draw a real tree (PileUp just calculates a pretty-looking 
UPGMA tree from the same pre-multiply aligned info).  HOWEVER, 
Clustal goes further in that you can then calculate a 
neighbour-joining tree from MULTIPLY aligned sequence pairwise 
comparisons (a whole lot more accurate - all the gaps are in the 
same places in each sequence relative to any other).  You should be 
able to get it for VAX and for MAC and for PC 
at the EMBL site.

Do you have more info about the above program?  I'm just learning to get 
around the network, how do I get it from 'the EMBL site'? Do I need another 
program to convert the 'tabular data' into a 'real tree'?   

Julie Knott
jknott at molbio.umn.edu
Dept of Cell Biology and Neuroanatomy
University of Minnesota

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