| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T269 |
0-36 |
Sentence |
denotes |
Comparisons to SARS-CoV-2 phylogeny. |
| T270 |
37-284 |
Sentence |
denotes |
Phylogenies downsampled at 10% from the full (18,514 tips) SARS-CoV-2 genome phylogeny (following the subsampling strategy described above) were used to calculate the phylogenetic η for each subtree (above the root) for each downsampled phylogeny. |
| T271 |
285-450 |
Sentence |
denotes |
Neutral phylogenies were simulated under stochastic branching by randomly sampling from the distribution of branch lengths from one downsampled SARS-CoV-2 phylogeny. |
| T272 |
451-515 |
Sentence |
denotes |
This was iterated across all downsampled SARS-CoV-2 phylogenies. |
| T273 |
516-786 |
Sentence |
denotes |
Positive time-dependent phylogenies were simulated using a time-dependent process (b(t)=0.01eαt) for α = 0.001, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, and 1, with branch lengths restricted to the distribution of branch lengths from one downsampled SARS-CoV-2 phylogeny. |
| T274 |
787-862 |
Sentence |
denotes |
This was iterated across all downsampled SARS-CoV-2 phylogenies for each α. |
| T275 |
863-955 |
Sentence |
denotes |
Neutral and positive time-dependent phylogenies were simulated with a 10% sampling fraction. |
| T276 |
956-990 |
Sentence |
denotes |
Polytomies were randomly resolved. |
| T277 |
991-1064 |
Sentence |
denotes |
Simulations were conducted using the R packages RPANDA (61) and ape (53). |
