[BiO BB] Phylogenetics

[Tucker, James]

Hi all,
We have a sequence that encompasses two genes. When drawing up a tree from
these sequences for several sub species of the same genus- we end up with a
tree that does not reflect the results we would anticipate (from our current
knowledge of the species, through RFLP, classical techniques, PCR RFLP etc).
The genes are both outer membrane protein - the problem seems to lie in the
fact that the genes are highly similar (85%) they can be in any order, there
may be duplication of one or other gene and the other gene is not present. 
One possible solution we can think of for this is to build a tree based upon
weighting: 
Either on secondary structure or gene expression.
Does anyone know of any software that we would be able to carry this out
with or alternative approaches.
Obviously we don't want to ignore these events as they are obviously
significant - we just want to be able to take them into account
proportionally.
Regards
James  


James Tucker
Brucella Research Group
Department of Bacterial Diseases
VLA Weybridge
Woodham Lane
New Haw
Addlestone
Surrey
KT15 3NB

Tel: ++44(0)1932 357227
Fax: ++44(0)1932 357873

mailto:j.d.tucker at vla.defra.gsi.gov.uk







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