To cite vivaldi in publications use:

Roder, A. E., et al. Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data. bioRxiv (2022): 2021-05 URL https://www.biorxiv.org/content/10.1101/2021.05.05.442873v2

Corresponding BibTeX entry:

  @Article{,
    title = {Optimized Quantification of Intrahost Viral Diversity in
      SARS-CoV-2 and Influenza Virus Sequence Data},
    author = {AE Roder and KEE Johnson and M Knoll and M Khalfan and B
      Wang and S Schultz-Cherry and S Banakis and A Kreitman and C
      Mederos and J-H Youn and R Mercado and W Wang and D Ruchnewitz
      and MI Samanovic and MJ Mulligan and M Lassig and M Łuksza and S
      Das and D Gresham and E Ghedin},
    journal = {bioRxiv},
    year = {2022},
    url =
      {https://www.biorxiv.org/content/10.1101/2021.05.05.442873v2},
  }