Help with construction of phylogenetic tree.

J.M. Ossewaarde JM.Ossewaarde at rivm.nl
Thu Apr 16 04:12:58 EST 1998


Computer programs will not produce correct alignments of 16S sequence data.
You have to align sequences manually. A good place to start is the rRNA WWW
server at http://rrna.uia.ac.be/ . You can download prealigned sequences
from this database.


--
J.M. Ossewaarde, MD, PhD
Research Laboratory for Infectious Diseases
National Institute of Public Health and the Environment
PO Box 1
3720 BA Bilthoven
The Netherlands
Phone: +31 30 274 3942
Fax: +31 30 274 4449
Email: JM.Ossewaarde at rivm.nl

Thibaud Le Mouël wrote in message <6h4a91$rs0 at mserv1.dl.ac.uk>...
>>I have two 16S rDNA sequences (complete), which I obtained by
>>sequencing both strands from two isolates. I want to construct a
>>phylogenetic tree by including these 2 sequences and other related
>>sequences.  I don't know if I need to align my sequences MANUALLY with
>>other selected sequences. I don't know why and how to do manual
>>alignment.  Does anyone know any reference on the basics and how to do
>>manual alignment?  Any info will be appreciated.
>>
>>It looks like people use fifferent program to construct such trees.  That
>>means with a same group of sequences, trees with different topologies can
>>be constructed.  I wonder if there is a "standard procedure and program"
>>that can used, at least in publication.
>>
>>
>>Zhongtang Yu
>>Dept. of Mcirobiology, UBC.
>
>You can use clustalX.PPC for both alignement and phylogenetic trees.
>
>Thib
>
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