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The problem can be avoided by using a relaxed conservation criterion rather than strict universality [ 22], but the problem of how to define a biologically meaningful core still remains.
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Substitution rates were estimated using a relaxed uncorrelated lognormal molecular clock [34].
Here, the ellipses were calculated using a relaxed criterion, outlining an area of just 50% probability.
Divergence time estimates among seahorse lineages were obtained using a relaxed molecular clock method [ 58].
Continue moving up scales a half-step at a time, using a relaxed jaw and tongue.
These observations suggest that the use of synteny information with a relaxed conservation criterion (CONS_RATIO < 1) helps the CoreAligner program to identify robust and reliable core gene sets, although the setting of the CONS_RATIO parameter still remains somewhat arbitrary.
Actually, we used a relaxed criterion for syntenic conservation (CONS_RATIO < 1) in our core genome alignment procedure.
Whereas paternally expressed genes are conserved at similar level as biallelically expressed genes, maternally expressed genes show a relaxed conservation.
Relaxed on-demand expansionThe second improvement is to use a relaxed on-demand expansion that reduces the need of exhaustive expansion and sorting operations.
We used a relaxed clock model, drawing substitution rates from a lognormal distribution.
Consequently, as suggested by Drummond et al. [ 50], we used a relaxed molecular clock.
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CEO of Professional Science Editing for Scientists @ prosciediting.com