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Best way to draw phylogenic tree

Yang-Seok Kim yskim at WWW.BRIC.POSTECH.AC.KR
Sun Mar 9 06:23:23 EST 1997

Hello !
I am a graduate student in POSTECH, South Korea.
Recently, I have cloned interesting gene in Brassica napus(plant) involved
in the synthesis of thiamin.
I have found it's very interesting in evolutional aspect.
In microbial genome, genes involved in the syntehsis of thiamin are existed
in a few sets of gene clusters, but in plant and yeast, two genes are
joined, so bifunctional genes are evolved.  However, the gene structure of
yeast and plant are very different.
So, I wish to draw phylogenetic tree of the thiamin biosynthesis to get
information about the evolution of thiamin biosynthesis.
For global allignment, I have used ClustalW1.6, MAP and PIMA1.4 and
protpars(parsimony algorithm) in PHYLIP for drawing phylogenic tree.
However, the three results of global allignment gave different alligned
results, so generated different phylogenic tree.
Which method is the best among them ?
I think one of the major reason is initial(N-termianl) and
final(C-terminal) gap among sequences.
Is it possible to rule out initial and  final gaps ?

Thanks in advance,

Yang-Seok Kim
Dept. of Lifescienc
POSTECH, South Korea


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