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Table S1 summarizes the number of start order loci, fixed order loci, and markers used to reconstruct the 10-5 map (File S4).
Between 11 and 28 start order loci were selected for each LG.
The regression mapping algorithm with modified settings (recombination frequency threshold < 0.49, LOD threshold > 0.01) was used to order loci within each linkage group.
Due to the large number of markers in the two NAM populations, we used the maximum likelihood mapping algorithm to order loci.
Reconstruction of the 10-5 map by specifying subsets of fixed and start order loci and removing loci with suspect linkages produced a map that was collinear with the other input maps and the consensus map.
Start order loci were then identified based on their being separated by more than 5 cM, having the highest genotype information content among neighboring loci, and having marker orders not in conflict with the BC1/QTL-BASE2 reference map order.
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Distances between ordered loci (in centimorgans) were calculated using the Kosambi mapping function.
The BUILD command was implemented by entering two linked, informative markers with recombination fractions of between 0.1-0.2 0.1-0.2red loci, asd inserting the remaining lordered
The most obvious approach, which is non-parametric, involves rank-ordering loci according to their value of a test statistic that is sensitive to selection, and designating significant loci as ones that are outliers from the distribution.
Pilot maps for individual populations were built by ordering loci with RECORD [ 26] to identify potential DNA sample-tracking errors between laboratories and to remove unreliable lines and loci.
Two or three loci with the highest number of informative meioses were chosen as the ordered loci and additional markers in the group were sequentially incorporated one by one at every possible location.
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