Final answer:
Scientists compare DNA sequences by obtaining the sequences of interest and comparing them with existing sequences in databases.
Step-by-step explanation:
When comparing DNA in molecular phylogeny, scientists obtain the sequences of interest and compare them with existing sequences in databases like GenBank. Computational tools are used to align and analyze the sequences, determining the percentage of sequence identity or homology. This sequence homology helps estimate the evolutionary distance between DNA sequences and reflect the time elapsed since they separated from a common ancestor. Molecular analysis has revolutionized phylogenetic trees by confirming or rearranging relationships based on DNA analysis.