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Quantitative analysis of congruence was performed using the SH test on the ML trees for combined C. coli data, C. jejuni/C.
Our analysis of congruence between the MIRU-VNTR, spoligotype and LSP results demonstrates that the LAM lineage is composed of at least three different main clonal branches, referred to as LAM I to III in this study.
(1) Direct comparison between MLST and MLVA based on 40 isolates, (2) indirect comparison of MLVA with MLST based on the data derived from the Ridom database, (3), circumstantial evidence that pvl genes were only present in MC8, MC30 and MC80, (4) in silico analysis of congruence using 14 fully sequenced genomes.
Analysis of congruence among the gene phylograms was performed on consensus trees, and 1000 trees created with random topology.
Moreover, the analysis of congruence between COI and ITS1 gene trees reveals signatures of coevolution between both genomes.
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Because of the highly clonal nature of M. tuberculosis [31], [39], [40], the analysis of the congruence between sets of fully independent markers is a relevant approach to identify strain lineages (e.g. [41], [42]).
Table 5 displays results from the analysis of couple congruence.> -wrap-foot> *Mann–Whitney U-test.
The analysis of phylogenetic congruence among all genotypes using the partition homogeneity test strongly suggested the occurrence of recombination within the population.
Consensus sequences of COI and 28S were created by collapsing all sequences from the same species using BioEdit 7.0.5, and used in the analysis of the congruence of parasite and host phylogenies.
And second, we introduce a procedure to complement the ml-FFR approach (used by Doyle to infer species boundaries from several markers) with an analysis of the congruence between markers, by scoring each possible bipartition of the set of individuals according to the number of independent marker supporting it.
In the O'Connor meta-analysis, the range of congruence with consensus solution for each individual dataset went as low as 0.60, but the mean congruence was around 0.80 for individual datasets with the consensus solution.
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