Based on the principle of taxonomic congruence that focuses on deriving a consensus from the results obtained from separately analyzed data sets, I think it's best to work with different methods of phylogenetic reconstruction, such as maximum parsimony, maximum likelihood, distance methods and bayesian inference

I would use MrModeltest to determine the model of evolution and then MrBayes to construct the phylogenetic tree by using Bayesian Inference.

A good reading in models of evolution

http://darwin.uvigo.es/download/papers/b04.modelPhylHandbook03.pdf

First you can do BLAST of the sequences obtained to align them with there closest relatives according to the sequences similarities and dissimilarities.

Then you can do a virtual PCR to confirm the relationships.

Following that you can do fingerprinting and phylogenetic studies to further confirm and outline the relationships.