After removing poorly aligned columns we obtained an alignment containing 848 nucleotides that was used for the estimation of long-term begomovirus substitution rates.
Thus, the algorithm was evaluated starting from low resolution with the aim of obtaining an alignment with rotation and translation errors of less than 5° and 5 mm, respectively.
Thus, this study guided us to obtain an alignment for generating Model 2 (using alignment in Fig S2B).
Finally, chain filtering is used to bring similar extended seeds together, and a gapped extension is performed to obtain an alignment from the extended seed that contains gaps.
Finally, for d = 15, we can obtain an alignment with a score slightly better than without the filter, while still being 14 times faster.
We obtained an alignment of Pol proteins from a total of 48 elements including the 15 elements isolated in this study.
To locate human-specific substitutions and indels we first obtained an alignment consisting of human (hg19), chimpanzee (panTro2), gorilla (gorGor1), and orangutan (ponAbe2).
For d = 14, we can obtain an alignment with a score quite better than without the filter (406 rather than 263), with an overall execution that is 66 times faster.
For 88% of the transcripts, we obtained an alignment with a BAC sequence, which, excepted for five transcripts, was localized on pig chromosomes allowing 33 more transcripts to be localized on chromosomes.
In each step of the iterative refinement process (Barton and Sternberg, 1987 ; Berger and Munson, 1991 ; Gotoh, 1993 ), an alignment is divided into two sub alignments and then the two sub alignments are realigned, according to the tree-dependent iterative strategy (Gotoh, 1996 ; Hirosawa et al., 1995 ), to obtain an alignment with a higher objective score.
