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CLUSTALV:??

Kai-Uwe Froehlich cbkfr01 at mailserv.zdv.uni-tuebingen.de
Thu Sep 8 09:13:50 EST 1994


In <Pine.3.89.9409052227.B22268-0100000 at molbio.cbs.umn.edu> jknott at MOLBIO.CBS.UMN.EDU (Julie Knott) writes:


>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.


>Ed, 
>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'?   

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

For Macintosh users, an easy to use program to draw phylogenetic
trees from numeric data is the Hypercard stack "Tree Draw Deck" 
from Don Gilbert. It produces unrooted and different flavours of
rooted trees which can be saved as fully editable PICT files 
(so you can correct overlapping names etc.). It does not accept
the output of ClustalV, so I wrote a little (4 k) Hypercard stack
"ClustToTree" which converts from the ClustalV format and allows
you to edit the names of the branches (ClustalV truncates them
after 10 letters). Both programs are available from Bio.Indiana
and EMBL-Heidelberg:

<ftp://ftp.bio.indiana.edu/molbio/mac/treedraw-old.hqx>
<ftp://ftp.bio.indiana.edu/molbio/mac/clustaltree.hqx>

<ftp://ftp.embl-heidelberg.de/pub/software/mac/treedraw.hqx>
<ftp://ftp.embl-heidelberg.de/pub/software/mac/clusttotree.hqx>

Kai-Uwe Froehlich

Kai-Uwe Froehlich, Physiologisch-chemisches Institut, 
Hoppe-Seyler-Str. 4, 76072 Tuebingen, Germany
kaifr at mailserv.zdv.uni-tuebingen.de




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