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I want to determine if there is horizontal gene transfer between two genomes, in particular I was to use the parametric methods described in wikipedia since I would most likely struggle to understand the phylogenetic methods fully.

The two genomes in mind would be Lactococcus lactis and Lactobacillus helveticus since they are used in the process of cheese making and therefore would be in close enough proximity/environment to argue for tentative events of HGT. (Correct me if I am way off base here in my line of thought...)

Could I just access representative genomes for each from NCBI and calculate/determine the various genomic signatures that are indicative of HGT via the previously mentioned parametric methods(Nucleotide composition, oligonucleotide spectrum, structural features, etc...)?

Or would the genomes need to be rendered and sequenced from a confirmed source where they are both located/habituated to properly argue for HGT?(In which case I believe NCBI does not have this data readily available?)

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Since the parametric model is applied to only a single genome to see if there is evidence of recent HGT via a change in the average content in coding regions, it will not tell you from where the HGT came from, just that a HGT likely occurred in an area of the genome. Since you are trying to specifically see if there was a HGT between L. lactis and L. helveticus you would have to run a parametric analysis on both, find a HGT candidate on one of the genomes and then find that sequence as a non-HGT candidate on the other genome and via BLAST.

These papers give a good argument to why to use genome signatures instead of GC content as a parametric method of detecting HGT.

Review from where most of the Wiki figures came from

Genome signature paper

Newer Genome signature paper

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