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All point mutations were converted to binary data (0 = no mutation, 1 = somatic mutation) for each sample, and a matrix with sample names in rows and loci in columns was generated.
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Surprisingly, the originally stable ben1-1 mutation was converted to a partial loss-of-function mutation in the triple mutant background.
The PMA1 URA3 variant was created from the pma1Δ::KanMX4/PMA1 strain; the ura3Δ0 mutation was converted to URA3 via PCR amplification of URA3 from pRS306 and transformation.
Three clones, X63 (with the mutations H97Y and S100aT), X64 (with the mutation S100aR), and X65 (with the mutations H97Y and S100aR), were converted to scFv formats and expressed in Pichia.
The migration parameters estimated by IM (m1 and m2), which represented the number of migrants per mutation (m = m/μ), were converted to population migration rates (M = 2 Nm = θ m/2).
The ancestral strain was converted to the evolved morphology by converting ancestral alleles to those of the putative causal mutations and the evolved strains were converted to the ancestral morphology by converting the putative causal mutations to their ancestral alleles.
Mutation scaled migration rates (M) were converted into Nm (number of migrants per generation) via θ1M2->1 = 4 Nm1.
During this process, mutations with an amino acid location were converted into those with a genomic location, and amino acid residues were converted into 3-mer nucleotide alleles, after which the mutation subtypes were determined.
In a pre-processing step, these diverse data types were converted into a single two-dimensional binary "mutation" matrix.
The calculated KS values of the 2-member gene clusters were converted to divergence time, using a substitution rate of 6.5 × 10−9 mutations per site per year34.
The Θ-values were converted to Ne using the formula Θ = 4Neu (u is mutation rate).
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