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Genetic dissimilarities between accessions were calculated using the simple matching coefficient in DARwin software [51].
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In addition, pairwise genetic distances between rice accessions were calculated based on the similarity coefficients following Nei and Li ([1979]).
The genetic distances between the 18 rice accessions were calculated with the "restdist" program of the PHYLIP (v. 3.67) package http://evolution.genetics.washington.edu/phylip.html; we used the distance matrix to calculate the coefficients of correlation with the metabolic diversity matrix and to calculate a phylogenetic tree by the UPGMA method using the "neighbor" program of PHYLIP.
The genetic distances between all combinations of any pairs in the 663 tomato accessions were calculated based on the genotypes of the 1248 SNPs.
Expression distances among accessions were calculated from the log e of fold change between treatments.
Overlap between these DMRs and 'temperature DMRs" calculated for the accessions was calculated and significance testing (Fisher's exact test) was calculated using R software.
GC content and sequence identity of ITS regions within heterogenous accessions was calculated using BioEdit (http://www.mbio.ncsu.edu/BioEdit/bioedit.html).html
Local metabolic diversity among the 18 accessions was calculated as a Euclidian distance matrix in each of the 104 bins.
The polymorphism information content (PIC) based on the 21 Physcomitrella accessions was calculated for all 64 SSR markers.
The relative kinship matrix comparing all pairs of the 472 accessions was calculated using the software package SPAGeDi.
Pairwise distances between all sequences from a given accession were calculated using the maximum composite likelihood nucleotide substitution model implemented in MEGA version 4 [ 73].
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