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We used two related measures for tree comparison, the Robinson-Foulds (RF) score [25] and the branch score (BS) [26].
With a low substitution rate, the mean branch score accuracy of all methods was roughly the same (except for MSN, which once again was significantly higher).
A Perl script (Phylip_tree_distance.pl) was used to run the PHYLIP treedist program to determine the distance between the RA and MLST trees using the Branch Score Distance [33].
Equation (11); RBS: Rooted branch score.
Equation (8); RH: Root height; SRBS: Squared rooted branch score.
Branch Score Distance (BSD) between the optimal AAF tree and trees generated with larger k.
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The Robinson-Foulds [ 26] distance and branch scores [ 27] between the two phylogenetic trees for the 10,075 genomes were calculated with the R package APE [ 49].
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