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.
Horizontal gene transfer is common in bacteria:
https://en.wikipedia.org/wiki/Horizontal_gene_transfer
thus just finding a new gene in a bacteria would not be indicative of genetic engineering.
What I would say here, is that if you find an "interesting" transgene sequence in a bacteria, that is really out of place and makes no sense, and depending on what that gene is and how it fits with the rest, you could explore the possibilities there.
After all, bacteria are the easiest organisms to manipulate in labs.
In my not-so-well-informed opinion, an analogy would be that bioinformatics is still working on confidently removing typos and what you're asking it is akin to the job of a newspaper editor. No matter what bioinformatics says, wet bench research is required to back it up. With that level of questioning, where we can only say with a certain amount of confidence if something we see if real, how can bioinformatics be expected to predict who created that reality?
how to prove that genetic engineering was successful by using bioinformatics tools?
What experimental data you are going to apply bioinformatics tools to? RNAseq (to show that the gene is expressed) or DNAseq (to show that the gene is present without being able to say if it is working)? Bioinformatics is only providing tools. You will still need to design/think of a proper experiment to apply the right tools. You may be able to get by without bioinformatics if there is a phenotype/growth characteristic you can easily monitor.
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It is an interesting question, with many complex answers. While there may not be a singular, foolproof way to tell that, depending on the particular case, there could be hints that could indicate genetic engineering.