Closed 326reborn closed 3 years ago
Hi. There is no deep justification for the cutoff being +/-0.1. A relatively broad range was selected to reflect RED being an approximation of time of divergence, the desired to retain the current placement of the majority of taxa, and the desire to have taxa on well-supported nodes.
Thank you for such a quick reply! So it means we should adjust this cutoff according to the feature of taxa we interested in like ciliates. Can I understand as this?
It can certainly be adjusted with the goal of picking an interval that allows the majority of existing taxa to be retained while providing a reasonable level of normalization across the tree. This is ultimately a tradeoff. On the one hand, retaining existing names is important as they are widely recognized and changing them hampers scientific communication. On the other hand, the goal of RED is to provide a quantitative criteria for defining ranks which normalizes taxa such that all taxa at the same rank arose at (roughly) same time in the past.
Hello, When I caculate the RED for each taxa, I find that taxonomic ranks were set as median RED ± 0.1 in the PhyloRank and your paper. I wonder why it's 0.1 ranther than other cutoff?
Thanks Yu Zhang