zoharyi were used to calculate genetic diversity indices and haplotype networks and to investigate population size changes and structure. Three secondary calibrations were used to estimate the timing of the divergence of B. zoharyi from its hypothesized sister species, B. elegans , and the ...
The formula to calculate the Aitchison distance between two generic vectors x and y of length m is: dA x, y = 1 m−1 m ln xi − ln yi 2 m i=1 j=i+1 xj yj (9) As for SMAPE, we computed Aitchison distance on CPM transformed data. For each dataset and for each pipeline,...
Background subtracted element signals were used to calculate Cy3:Cy5 ratio. The average of the resulting total Cy3 and Cy5 signal gave a ratio that was used to balance or normalize the signals. Oligonucleotide microarray analysis The HU 6800 microarray was obtained from Affymetrix (Santa Clara, ...
2007) was used to calculate the polymorphism information content (PIC) and to create input files for the software GENEPOP ver. 4.2 (Raymond and Rousset 1995; Rousset 2008) to conduct Hardy–Weinberg Equilibrium (HWE) testing; dememorization number = 5000; number of batches = 1000; ...
to be effective when describing small-scale/narrowly defined conformational transitions, the vast phase space associated with accommodation makes it computationally intractable to calculate the free energy. In contrast, through the use of simpler models, one may evaluate and compare the free energy of ...
2012) to calculate most diversity statistics directly from the OTU table. Bacterioplankton richness and abundance was compared between depth horizons using ANOVA (function aov), and depth horizon means were compared using Tukey post hoc tests (function TukeyHSD). Samples from the deepest depth ...
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The formula to calculate the Aitchison distance between two generic vectors x and y of length m is: [Math Processing Error]dA(x,y)=1m∑i=1m−1∑j=i+1m(lnxixj−lnyiyj)2 (9) As for SMAPE, we computed Aitchison distance on CPM transformed data. For each dataset ...
In the positive selection analysis, only above single copy genes were considered. To calculate the nonsynonymous (Ka) and synonymous (Ks) substitution rates between pairs of orthogroups, above amino acid alignments were reverse-translated to the corresponding codon-based nucleotide alignments by PAL2NAL...
(mol. mass. cutoff 3 kDa, concentrator Pierce PES 3K, Thermofisher). The concentration factor was noted for each fluid and used in the calculation of the results. The average concentration factor was 7 with a range from 4 to 10 and it was used to calculate non-concentrated levels. A ...