Example data results in different phylogeny compared to nextstrain homepage

Help and Getting Started
1

Hi, when running the example data of the ncov tutorial (Run using example data — SARS-CoV-2 Workflow documentation) it results in a different phylogeny compared to the one shown on the nextstrain homepage (auspice).

In the example data, BA.1 clusters closer to Gamma or Theta while it is closest to Delta on the nextatrain homepage. What is the reason for this? My output of the example data matches what is shown in the figure of the tutorial.

Thank you.

2

Where Omicron attaches depends a lot on which sequences are included and how the tree builder happens to explore tree space - it’s a complex optimization problem and sequences are not 100% clean.

The example data is very simple and not intended to be used as a real analysis, it’s meant to provide enough to get started with nocv.