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The table reports, for each alignment, the size of the aligned complexes and the ISC (Index of Structural Conservation) score.
For each alignment result we calculate the percentage of aligned reads.
For each alignment, we examined the Ensembl genes nearby the aligning fragment in each species.
Out of the four aligners, BWA and Novoalign both have a mapping quality score reported for each alignment.
A single representative structure was chosen for each alignment.
For each alignment, we performed two searches using different models of sequence evolution.
A single representative structure was chosen for each alignment without regard to the coevolution results.
The counts for each alignment were sorted into a 20×20 matrix.
Ideally such a scoring function should provide a statistical significance value for each alignment as well.
Two scores were calculated for each alignment, based on inclusion or exclusion of gaps in the alignment.
For each alignment, a preliminary tree was drawn.
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