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This copy number divergence was partly attributed to duplication events within each genome.
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The relationship of the paired-taxa measurements of LCNS numbers, divergence time, and d S can reveal patterns of evolutionary rates of LCNS retention between species.
Again we tested allele number, allele divergence and ABS divergence independently.
Three different estimates for MHC diversity were used independently because of co-linearity: allele number, allele divergence and ABS divergence.
Recently, Oaks et al. [ 7, 15] found via simulation that msBayes will often strongly support models with a small number of divergence events shared among taxa, even when divergences were random over broad timescales.
In the limit as the number of divergence points d increases and the proportion of diverging sites θ decreases, the model approaches the covarion model.
The number of divergence events within host groups was many more than expected by chance revealing a pronounced pattern of repeated divergence of this trait within host groups and broad scale convergence across the radiation of feather lice.
I constructed these plots using two criteria for the one-divergence model: (1) the number of divergence-time parameters (| τ |=1) and (2) the dispersion index of divergence times (D T <0.01).
Figure 7 also shows the prior distribution across the number of divergence events for each model, as well as the average prior probability of an unordered and ordered model of divergence (t ) across | τ |.
Oaks et al. [ 7] discuss how placing a uniform prior over the number of divergence parameters (denoted | τ | here, and as Ψ in [ 4]) imposes an "U-shaped" prior over divergence models (t; see Figure five(B) of [ 7]).
Due to their specific dynamics during genome evolution, TE families may differ considerably in terms of copy number, sequence divergence and insertion/deletion patterns.
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