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methods and parameters in constructing phylogenetic trees ??

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methods and parameters in constructing phylogenetic trees ??

Postby bass_lasso9 » Wed Dec 09, 2009 4:02 am

I am doing research in dna barcoding,,
but..
I am still curious about constructing phylogenetic trees..
many journal articles in molecular sytematic fields (including dna Barcoding) interpret the data using various methods and parameters,,
like Neigbor-Joining, Maximum Parsimony, maximum Likelihood, etc. and parameters like Kimura-2-parameter, Tamura-Nei, Tamura, etc.

what method and parameter which is best to be used?
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Postby mith » Fri Dec 11, 2009 2:06 am

there is no best parameter, you have to determine which model and which method is appropriate for a given set of sequences
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Postby JackBean » Sat Dec 12, 2009 3:46 am

Each method/parameters are suitable for some application.
E.g. in alignment, BLOSUM is suitable for homologous sequences, while PAM is better for phylogenetic analysis. And the same here. What is your goal? That will decide.
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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