The tree is a severely pruned version of the UCSC tree (2023-10-15) re-rooted to lineage A with 50 randomly selected descendants per lineage. Also adding adding latest designation hash and alias file corresponding to v1.23
*** NOTE: the v1.23 tree provokes a corner-case bug in usher-sampled prior to version 0.6.3 that affects samples whose best placement is at the root of the tree, i.e. lineage A (early 2020). If you will be running pangolin on early 2020 sequences that may be lineage A, then it is highly recommended to use the assignment cache (install by running pangolin --add-assignment-cache, run pangolin on input sequences with --use-assignment-cache) and to update the usher package in your pangolin environment to 0.6.3 as soon as it is released.
The tree is a severely pruned version of the UCSC tree (2023-10-15) re-rooted to lineage A with 50 randomly selected descendants per lineage. Also adding adding latest designation hash and alias file corresponding to v1.23
*** NOTE: the v1.23 tree provokes a corner-case bug in usher-sampled prior to version 0.6.3 that affects samples whose best placement is at the root of the tree, i.e. lineage A (early 2020). If you will be running pangolin on early 2020 sequences that may be lineage A, then it is highly recommended to use the assignment cache (install by running
pangolin --add-assignment-cache, run pangolin on input sequences with--use-assignment-cache) and to update the usher package in your pangolin environment to 0.6.3 as soon as it is released.