To cite vivaldi in publications use:

Roder A, Johnson K, Knoll M, Khalfan M, Wang B, Schultz-Cherry S, Banakis S, Kreitman A, Mederos C, Youn J, Mercado R, Wang W, Ruchnewitz D, Samanovic M, Mulligan M, Lassig M, Łuksza M, Das S, Gresham D, Ghedin E (2022). “Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data.” bioRxiv. 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},
  }