| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T226 |
0-178 |
Sentence |
denotes |
The global phylogeny was reconstructed in FastTree v2.10.1 compiled with double precision under the GTR model with gamma heterogeneity (51), and rooted at the reference sequence. |
| T227 |
179-226 |
Sentence |
denotes |
The tree was visualized using ggtree in R (54). |
| T228 |
227-457 |
Sentence |
denotes |
Lineages were defined using PANGOLIN (Phylogenetic Assignment of Named Global Outbreak LINeages), with lineages with >200 taxa as of the May 19 summary being highlighted in the tree (22) (https://github.com/cov-lineages/lineages). |
| T229 |
458-638 |
Sentence |
denotes |
The number of polymorphic sites was calculated as the number of sites which had at least one mutation relative to the reference sequence, Wuhan-Hu-1, ignoring gaps and ambiguities. |
