A computer simulation analysis of the accuracy of partial genome sequencing and restriction fragment analysis in the reconstruction of phylogenetic relationships

A computer simulation analysis of the accuracy of partial genome sequencing and restriction fragment analysis in estimating genetic relationships: an application to papillomavirus DNA sequences

“…However, another study from our laboratory [15], using simulated genomes of various size with different nucleotide substitution rates, and varying degrees of genetic diversity among samples, found that only under conditions of both short partial genome sequence length and low rates of nucleotide substitution did RFA provide a more accurate topological reconstruction of phylogenetic relationships than did partial genome sequencing; the degree of genetic diversity among samples did not affect the advantage partial genome sequencing had in accurately depicting phylogenetic relationships. Thus, whether one is investigating the genetic relatedness among samples collected from a single disease outbreak or a diverse collection of samples from different times and geographic regions, under most conditions partial genome sequencing will represent genetic relationships more accurately than does RFA.…”