In these cases, the p-Cytb and the pseudo copies of tRNAPro1, ND6, tRNAGlu1 and tRNAThr2 are usually decayed beyond recognition.
As only one pseudogene copy was obtained from each examined line, differential loss would have to remove all but one pseudo-copy in each lineage, which is perhaps unlikely.
Since this set might contain pseudo-copies generated by unrelated sequences, it is processed by the following two steps to eliminate pseudo-copies.
2. Detected unrelated sequences derived from other LTR elements and eliminated their pseudo-copies.
Therefore, we developed an algorithm (see Methods) to discriminate unrelated sequences and discard the matches generated by them (pseudo-copies).
These many potential sources of rate variation could greatly exacerbate the phylogenetic uncertainties caused by extra pseudo-copies.
Accordingly, the matches generated by such subregions were eliminated from Part II. 3. Detected unrelated sequences derived from other TEs and eliminated their pseudo-copies.
Although this simple greedy algorithm might fail to deal with a few complicated situations, it identified most of the pseudo-copies efficiently.
The annotation process identified unrelated TE sequences in elements and discarded pseudo-copies, thus estimated the contribution of LTR elements to the genome more accurately.
We first identified candidates of full-length element with LTR_FINDER, then annotated other copies related to them in the genome by homology search and the elimination of pseudo-copies.
Here ( left { Delta W^{n}_{t_{k}}: k=1,2, cdots, nright } ) simulates, by pseudo random numbers, independent copies of centered Gaussian random variables with variance n−1. 3.
