My colleages and I am working on ancient pathogens and we would like to use Nextstrain to display our ancient pathogens with their modern counterparts and to show the evolution of the pathogen over time.
So far, it was fairly easy to set up the pipeline to obtain a tree, however we have run into a problem. In our dataset we have ancient genomes that predate the year 0. Right now, we have set up the metadata for all the genomes that are older than year 0 to 00XX-XX-XX, however this is technically incorrect. We have been discussing to use the older sample as year 0 and include an off set of all the other genomes. An example of this concept will be: we have 3 samples in our dataset one being 5000 years ago, another being from year 2000 and a current one 2021. Our older sample (5000 years ago) will then become year 0 and in the date column will look like 00XX-XX-XX, the sample from 2000 will look like 7000-XX-XX and the one from this year (2021) will be 7021-XX-XX. This work around is however not ideal.
I would like to ask if you have any recommendations in how to deal with this and if it will be possible to include negative years as -XXXX-XX-XX.
Thank you in advance,