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The activity track corresponds to the probability of having a pairwise nucleotidic identity with the most identical pair of copies less than or equal to the expected identity, estimated using the reference distribution constructed from the global alignment of the two genomes.
We built an index of the similarity of each copy of these elements compared with the most identical pair of copies between the two genomes, normalized by the size of the copies.
These activity tracks are used to rank between 0 and 1 all the copies of each identified TE according to their divergence from the corresponding most identical pair of copies between the two genomes, with 1 corresponding to a low degree of divergence and a recent activity of this TE and 0 corresponding to old and divergent copies.
According to the activity track distributions, most of the detected TE families in our results presented a recent period of activity in D. melanogaster (supplementary figs. S2 and S3, Supplementary Material online), with a large number of copies highly similar to the most identical pair of copies between the two genomes (see e.g., the diver element, fig. 4 A).
For each TE family, this most identical pair of copies between the two genomes is defined as the pair of copies with the lowest P-values from all the detected copies using the 80-80-80 rulet(Wicker et al. 2007).
With the activity track ranking the TE copies according to the most identical pair of copies between the two genomes which can be seen as the last putative horizontally transferred copy in the case of an HT, we were able to balance the direction of the transfers, which is crucial to understand the horizontally transferred TE history and dynamics.
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