This is a fork of the full D68 Nextstrain run repository, with minor changes to run the analysis for this analysis, resulting in this paper link to be added.
To see the maintained, original verion of this code, please see here. A release version which corresponds to the version used here (without paper-specific changes, see below), can be found here.
For detailed changes specific to analysing the paper, please compare with this fork.
The changes are overall minor and include: adjusting input files to incorporate the new data, adjustments to colouring for better figures, duplicating columsn & adding meta-data at the end for better figures, adjusting credit for the build maintenance, and semi-manually fixing alignment issues to avoid splitting codons when aligning.