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We extend this approach in two ways: (1) using a grid-based landscape model, as described above, thus obviating the need for discrete waypoints, and (2) taking into account not only the divergent part of trajectories, but also the length of the shared part.
The more the generations, the smaller the expected length of the shared haplotype.
The length of the shared block appears to depend upon the divergence time.
Furthermore, the accuracy of a haplotype match between two individuals is mainly a function of the length of the shared haplotype and the number of matched SNP.
In cases where two orthologs share MDSs, the length of the shared regions is usually conserved relative to that in Oxytricha (all but 4 are similar within 50 bp or 10%, whichever is larger, of the length of the shared gene segments in Oxytricha).
For classification in terms of separation by landscape features, the premises pairs would only be classified as such if the entire length of the shared boundary appeared to be separated by this feature.
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We confirmed that there is a significant correlation between the lengths of branches for clades shared by the mtDNA and nucDNA trees using Spearman's rank correlation (r s = 0.53; P = 0.03), and between the lengths of the shared branches in the mtDNA and combined trees (rs = 0.96; P < 0.00001) and the nucDNA and combined trees (rs = 0.73; P < 0.0001).
The concatenated length of these shared regions was 1344 kbp.
However, the length of the segment shared between mutant carriers suggest that the mutation may be older than what has been predicted.
This parsimony method consists of selecting among the different possible haplotype reconstructions the one that maximizes the length of the haplotype shared by all variant carriers.
The length of the haplotypes shared by two individuals on a specific chromosome is a function of the number of crossovers that occurs in the genealogical path that connects them.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com