I have at hand whole genome sequences of two novel bacteria species. And I want to see their relationship with the already existed bacterial species. But the thing is I am not sure if I should construct NJ or ML or any other trees that will best describe my bacteria in relation to others. Is there an advantage using ML instead of NJ.
Aligning complete genomes of bacteria is as tough as building phylogenetic trees from a sampling of the aligned genes. Some bacteria have a high degree of synteny (same gene order in the genome) despite large differences in % identity between isolates. Other bacteria have many genome rearrangements even when many of the genes are 100% identical between species.
As Brain said, using the complete genomes maybe difficult and it would probably be easier to use a few selected genes (such as those used in MLST schemes).
With regard to your question of using NJ or ML, I would suggest doing both and comparing the trees to each other. I recently published a species announcement and during the review process was asked to rebuild the trees using a different algorithm to ensure that the trees were accurate.
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