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Following Lambert et al. (2002) and Millar et al. (2008), we define mutation rate as the rate at which a base substitution is incorporated into all mitochondrial genomes of an individual.
By manipulating the user-defined mutation rate and population size, we were able to simulate sequences under known values of θ.
We defined the mutation rate as "the percentage of mutant genome copies per sample".
We defined the mutation rate to be 1.5 × 10−8 and simulated 5000 haplotypes with 500 000 base pairs.
Every time that a sequence replicates, each of its nucleotides has a probability (defined by the mutation rate μ) to be replaced by another nucleotide, randomly chosen among the four possibilities.
This process is defined by the mutation rate μ and by the characteristic function M x) = Σ r > 0 m r cos (rx).
We define an overall mutation rate per gene and specify the relative ratio at which point mutations, duplications, deletions, and rearrangements take place.
Accordingly, we define the scaled mutation rate in the ancestral deme as θanc = 4 Ne u.
One of the main signals that we used to define the number and size of the blocks is the mutation rate, defined as the fraction of mutations per nucleotide in each block.
The way we quantify the mutational input is by defining a genome-wide mutation rate for fitness (U) and by assuming that replication of each new genome entails a variable number of mutations that is stochastic and, more specifically, will follow a Poisson distribution with mean U.
The mutation rate was defined as the probability of a cell undergoing a mutation in its lifetime and expressed per cell per generation.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com