Investigation of evolutionary relationships of plasmids by combining sequence alignments with genome signature

Current DNA comparisons focus on single gene alignments to reconstruct a phylogenetic tree. Standard phylogenetic methods based on sequence alignments are not always applicable to plasmids because many plasmids do not share homologous genes. To overcome this limitation, sequence alignment methods are combined with genome signature, facilitating the comparison of any DNA sequences regardless of the presence of homologous genes. Nucleotide alignment, amino acid alignment, and genome signature are integrated to combine vertical evolutionary history, which reflects shared ancestry with horizontal evolutionary, which reflects shared hosts.