An alternative approach would be to construct and test a parameter describing the degree of incompatibility (i.e. conflicting phylogenetic signals) between topologies. To the best of our knowledge, no such straightforward metric exists for this particular purpose of quantifying the level of incompatibility. Alternative topologies could be compared with a reference topology obtained from, e.g. the literature, a large set of concatenated genes or a source of high-quality whole-genome data. Ideally, such

reference topology should mimic the species phylogeny as accurate as possible. In this study, we evaluated the specificity of detection and classification of Francisella by first comparing published PCR primers against whole-genome sequences representing the known CDK inhibitor diversity of the genus. Second, we examined the sequence-marker robustness and resolution by comparing different sets of one to seven markers using a modified version of the RF metric. Finally, we showed that optimal sets of markers outperform other combinations with respect to phylogenetic robustness and resolution. Results Overall fit between DNA-markers and whole-genome sequences

of Francisella A total of 42 publicly available Francisella genome sequences were screened for sequences (Table 1) of 38 published markers (Table 2). 14 markers had incomplete sets of marker sequences (Figure 1). The lack of 16S marker sequences in FSC022, FSC033, MA002987, GA993549, and GA993548 was probably due to the low quality of the genome sequences, which were all sequenced with early versions of 454 sequencing Entospletinib ic50 technology. The lack of sequences for the remaining 10 markers was most likely because they were designed for real-time PCR molecular detection or possibly due to uncovered regions in the sequence (Additional file 1). Table 1 Genomes sequences included in the study Species ID BioProject ID F. tularensis subsp. YH25448 clinical trial holarctica FSC200 16087 F. tularensis subsp. holarctica FSC208 73467 F. tularensis subsp. holarctica RC503 30637 F. tularensis subsp. holarctica LVS 16421 F. tularensis subsp. holarctica FSC539 73393 F. tularensis subsp. holarctica

OR96-246 30669 F. tularensis subsp. holarctica FTA 20197 F. tularensis subsp. holarctica URFT1 19645 F. tularensis subsp. holarctica MI00-1730 30635 F. tularensis subsp. Cyclooxygenase (COX) holarctica OSU18 17265 F. tularensis subsp. holarctica FSC021 73369 F. tularensis subsp. holarctica FSC022 19015 F. tularensis subsp. mediasiatica FSC147 19571 F. tularensis subsp. mediasiatica FSC148 73379 F. tularensis subsp. tularensis FSC054 73375 F. tularensis subsp. tularensis ATCC6223 30629 F. tularensis subsp. tularensis FSC033 19017 F. tularensis subsp. tularensis MA00-2987 30443 F. tularensis subsp. tularensis FSC198 17375 F. tularensis subsp. tularensis SCHUS4 (FSC237) 9 F. novicida FTE 30119 F. novicida U112 16088 F. novicida FTG 30447 F. novicida GA99-3549 19019 F. novicida FSC160 73385 F. novicida FSC159 73383 F.