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Because there is no reliable neutral mutation rate available for other species or their close related taxa, these species were not included in this analysis.
Values of ρ and σ were converted to age estimates using the most recent mutation rate available for the HVS-I segment of one transition per 18,845 years (in the sequence range 16090 16365) (Soares et al. 2009).
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Since no estimates of COI mutation rate are available for bats, we did not use a fixed substitution rate but estimated minimum and maximum divergence times using two substitution models, 2% and 5% per million years, based on estimates for cyt b in small-bodied mammals [ 49].
Our example is human plague, but the approach could be applied to other diseases for which data on marker mutation rates are available (3 ).
Indeed, no reliable estimate for the mutation rate is currently available for mouse lemurs.
Because a neutral mutation rate is not available for silkworm, we applied an estimated mutation rate previously published in Lepidoptera (1.909 × 10−8/site/year; Simonsen et al. 2011).
This statistic is a powerful detector of recombination and has been shown by simulation studies to be less sensitive to the effects of mutation rate correlation than other available statistics, which are prone to falsely infer recombination when levels of recurrent mutation are high [ 25].
To dissect the relative contributions of replication and transcription on the extent of substitutional asymmetries, we used a set of 492 human genes where information for all three potentially explanatory variables the distance of the gene to its nearest ORI (variable β), germ line expression level (variable ε), and the relative mutation rate (variable τ)—is available.
A straight forward way to estimate the age of a particular "root" haplotype, given the mutation rate, is to consider all available descendant individual sequences and take the arithmetic mean over all distances to the root haplotype.
To our knowledge there was so far a single web-tool available for mutation rate calculation (Hall et al. 2009) but this tool does not allow to consider deviations from Luria Delbrück or to estimate the goodness of fit with the model.
One way to test this possibility is to estimate the mutation rates based on available data.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com