fish systematics

[Cecile Fischer]

What is the most appropriate method to establish a phylogenetic tree of closely related fishes ?
We have sequenced the mitochondrial 12S, 16S, cytochrome b gene and Dloop in several species of 
the same family. We tried some analyses with the PAUPsearch program (included in the GCG 
package) but we don't know which options parameters are the best. In fact, we are really not 
used with these calculations...

Could somebody give us some advices to do this job ?

Thanks very much.

Cecile FISCHER
Alain BERNOT

Centre National de Sequencage
FRANCE