Figure 1.
An example application of ClonalFrameML to a simulated dataset.
(A) The clonal genealogy produced by simulation. (B) Maximum-likelihood reconstructed phylogeny. (C) ClonalFrameML reconstructed phylogeny. (D) Representation of recombination events along the genome for each branch of the genealogy in (A). True events are shown in blue and events detected by ClonalFrameML are shown in red. Three branches of interest and their associated recombination events are highlighted by red boxes.
Figure 2.
Comparison of correct parameter values with estimates from ClonalFrameML for a hundred datasets simulated under the ClonalFrame model.
Dots represent the point estimates and bars the 95% confidence intervals. Colours represent the correct value of the compound parameter δR ranging from 10−3 (black) to 102 (red).
Figure 3.
Comparison of correct parameter values with estimates from ClonalFrameML for a hundred datasets simulated under the coalescent with gene conversion model of intra-population recombination.
Dots represent the point estimates and bars the 95% confidence intervals. Colours represent the correct value of the parameter δ ranging from 102 (black) to 104 (red).
Figure 4.
Application of ClonalFrameML to 86 genomes of C. difficile ST6.
For any branch of the genealogy and any position along the genome, inferred recombination is marked in blue.
Figure 5.
ClonalFrameML analysis of recombination in S. aureus based on 110 genomes representing carriage and reference isolates mapped to MRSA252.
Reconstructed substitutions (white vertical bars) are shown for each branch of the ML tree. Grey areas represent non-core regions of the MRSA252 genome. Dark blue horizontal bars indicate recombination events detected by the analysis.