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These models are expected to be able to accommodate high levels of rate heterogeneity, and therefore to perform better.
Both the UCLD and random local clock models indicated moderate to high levels of rate variation among lineages (as shown by the coefficient of variation parameter, Table 4), suggesting that a strict clock model was not appropriate for our dataset regardless of performance of the MCMC.
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Similarly, our simulation study showed that the high level of rate variation can not be explained solely by the fast turn-over rates of recently transferred genes (Additional file 11).
Of the 25 phylogenetic groups, 20 groups showed a fairly high level of rate variation for gene insertions/deletions among genes, and the confidence interval falls into a small range for each α value (Table 4).
Why it might have greater influence at higher levels of rate variation will be explored in future work.
Unlike the independent rates analyses, the correlated rates model did not perform well at higher levels of rate heterogeneity (σ = 0.2-2).
These analyses also suggest that a strict clock may be suitable at slightly higher levels of rate variation when multiple independent loci are available.
Given the high level of rating in Round 1 and the reduced number of items, Section A became a ranking exercise for participants to prioritise their responses to identify the key items for inclusion in the CAT.
Among these approaches, the GoldenGate assay developed by Illumina and relying on the bead array technology has demonstrated high performance with high levels of call rate, reproducibility, and overall success rate for the analysis of the human genome [ 29- 31].
Hereafter, the authors refer to the low, medium and high levels of unemployment rate in relative terms, which however corresponds to considerably different levels of unemployment rate across study regions.
Considering the extremely high levels of mutation rate of HIV-1, these findings suggest that strong selective forces are continually purifying the R5 viruses during long-lasting persistent infection.
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