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Ne was estimated using the program MNe [6], that allows the estimation of Ne from genotype data collected at different time points.
For a set of accessions, genetic diversity parameters such as number of alleles per locus, allele frequency, heterozygosity and polymorphic information index (PIC) was estimated using the program POWERMARKER Ver3.25 (Liu and Muse 2005).
Divergence times between and within Macaronesian chaffinches were estimated using the program BEAST v. 1.5.2 [61.5.2
Genetic distances among haplotypes were estimated using the program DNADIST of PHYLIP, based on Kimura-2-parameter model.
Carnivore densities were estimated using the program Transect, which compensates for differences in sighting distance between the grassland and shrubland habitats [66].
Density of deer mice at each site were estimated using the program DISTANCE (version 4.1) a software program designed to better estimate animal densities on web trapping designs than using the raw values [56].
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The mole fraction of components in type 2 fluid inclusions was estimated using the programs CURVES (version 12/02) and ICE (version 12/02), implemented in the package of programs CLATHRATES [30, 34].
Maximum likelihood trees were estimated using the programs PhyML [ 52] and RAxML [ 53].
The number of different AFLP genotypes and Nei´s genotype diversity [ 42] in the P. alpicola populations were estimated using the programs Genotype v1.1 and Genodive v1.2 [ 43].
Population-specific values of M (the number of alleles / the allele size range) and Mc (the critical value of M) were estimated using the programs M_P_VAL and CRITICAL_M (Garza and Williamson 2001), respectively.
Population clearance, volume of distribution, and the baseline magnesium concentration were estimated using the NONMEM program.
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