I finally got a decent-looking tree using back-translated protein sequences to align the nucleotides of bacterial genome regions that span (12-20)kb. I used NJ algorithm and Jukes-Cantor distance matrix + 100x bootstrap to build the tree. I've attached an image of the tree, and the sequences distantly clustered almost perfectly by species (S. pyogenes and S. Dysgalactiae) except in one instance (i.e., FCT-6). Could this be evidence or support for horizontal gene transfer? Please see attached image, thank you.
It could be HGT--you should look at the alignments themselves and see if there are highly conserved residues common to certain parts of the tree as well as looking at the tree topology based on overall similarity.
It might be, but a single tree analysis can by definition not say anything about hybridisation/HGT. Before you do anything else you may want to check the alignment for incongruences that may result from hybridisation - e.g. by plotting a splits network using the SplitsTree software (it reads the fasta file format). If you find something suspicious you may want to do more advanced tests.
Here's another way to visualize phylogenetic trees containing species of hybrid origin. The original insight came in a 1984 article in the same journal by Vicki Funk, who recognized that searching for patterns in homoplasies in phylogenetic trees was the key.
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