methods and parameters in constructing phylogenetic trees ??

[bass_lasso9]

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?

[mith]

there is no best parameter, you have to determine which model and which method is appropriate for a given set of sequences

[JackBean]

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.