
Is it enough to find a transgene sequence in the genetically engineered bacteria (via BLAST server) to confirm that the engineering was successful? In general, how to prove that genetic engineering was successful by using bioinformatics tools? Is the phylogenetic tree would be recommended? What else could you suggest?
If you are engineering a bacteria, you are probably working with a single-isolate culture. Then, the complete workflow would be: sequence the original strain, sequence the putative transformed strain - best to sequence both with PacBio or Nanopore, assemble both genomes. Then there is a number of analyses you should perform: align the genomes, search the transgenes in both genomes (with Blast or other program), check if the transgene is complete, if the marker gene (if any, e.g., some antibiotic resistance gene) is present, and so on.

If you are engineering an eukaryote, you can follow the same workflow, but the more complex the genome (e.g., some polyploid plants), the more difficult will be to fully characterize the transgene (where it inserted, how many copies, if it integral or not, etc). In this case, wet lab techniques can be faster and cheaper than sequencing plus bioinformatics.