I am using nextclade (https://clades.nextstrain.org/) for analysis of my Influenza HA nucleotide sequence, when I upload the fasta file and select reference " Influenza A H3N2 HA", in the tree it shows divergence on the x-axis but I need to add years on the x-axis instead. Please help me to figure out this.
@sekhwal thanks for reaching out!
Unfortunately, time-scaled trees are currently not supported by Nextclade. We have been discussing about this, but there are no immediate plans to implement this.
If you need a time scaled tree, you will need to run the Nextstrain pipeline or TreeTime.
see here for example:
https://treetime.readthedocs.io/en/latest/tutorials/timetree.html
Thank you for the suggestion. Can you please provide me some more help, on how to use nextstrain to add one my fasta sequence (H3N2 HA) and its metadata in Influenza A H3N2 HA and add time-scale on the phylogenetic tree?
Do I need to use GitHub repository (GitHub - nextstrain/seasonal-flu: Scripts. config, and snakefiles for seasonal-flu nextstrain builds) to add my fasta sequence? If you can suggest the steps and a particular document that would be appreciated.
If I download the GitHub repository, how to make it run, any build.yaml requires, please give me the command.