2.10 | Estimation of LTR insertion time
We used LTR_FINDER software accompanied by PS SCAN (Prestridge et al.
1991) software to identify LTR sequences whose score was greater than or
equal to 6 in the assembled Sulv 1 genome, and duplicate results were
filtered. Then the flanking sequences on both sides of the LTR were
extracted. After aligned with MUSCLE, DistMat was used to calculate the
distance based on Kimura model with the molecular clock selected as
7.3*10-9.