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This procedure is iterated until the highest scoring pair is no longer above the permissible linkage affinity (A>0.05).
We define this linkage affinity, A(C u, C v ), between two clusters as follows: where C k is the cluster consisting of X i and X j.
If the highest scoring pair is above the permissible linkage affinity, we unify them, and recompute the linkage affinities between the new cluster and all others.
We use hierarchical clustering (Fowlkes and Mallows, 1983), a greedy clustering algorithm that starts with each data element in its own cluster, and then merges the most similar clusters until no two clusters are above a predetermined linkage affinity.
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All graphical depictions of linkage group affinities were constructed using MAPCHART [ 36].
Both the M and B 3R lineages share several gnathostome ancestral linkage group affinities (i.e., E', andand B') [ 15].
Due to rearrangements within the genomes of these species, multiple smaller linkage group affinities are also evident for certain ancestral groups.
Only 5 homeologs were detected with an abundance of duplicates (≥ 5), and in total, only 19 homeologies are described, with 6 of these putative homeologs based upon inferences from the ancestral linkage group affinities.
These latter studies have comprehensively described whole-chromosome arm homologies between rainbow trout and Atlantic salmon, and extensive linkage group affinities between the ancestral ray-finned fishes and the duplicated chromosomes in salmon species.
Following a WGD six linkage group affinities would be expected in a 4R lineage which is consistent with the empirical data within archetype group M. For linkage group G/H, the current data is compatible with an interpretation that this assemblage could have arisen from two ancestral linkage groups.
Additionally, drugs or factors can be loaded in the gel via impregnation and tethering to the gel through covalent linkages or affinity-based systems.
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