The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
To cite the dowser package in publications, please use
Hoehn K, Pybus O, Kleinstein S (2022). “Phylogenetic analysis of migration, differentiation, and class switching in B cells.” PLoS Computational Biology. doi:10.1371/journal.pcbi.1009885, https://doi.org/10.1371/journal.pcbi.1009885.
If you use the [correlationTest](vignettes/Measurable-Evolution.md) function for measurable evolution, please also cite
Hoehn K, Turner J, Miller F, Jiang R, Ellebedy A, Pybus O, Kleinstein S (2021). “Human B cell lineages associated with germinal centers following influenza vaccination are measurably evolving.” eLife. doi:10.7554/eLife.70873, https://elifesciences.org/articles/70873.
If you additionally use [IgPhyML](https://igphyml.readthedocs.io) for building trees please also cite
Hoehn K, Van der Heiden J, Zhou J, Lunter G, Pybus O, Kleinstein S (2019). “Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination.” PNAS. doi:10.1073/pnas.1906020116, https://doi.org/10.1073/pnas.1906020116.
Corresponding BibTeX entries:
@Article{, style = {citation}, title = {Phylogenetic analysis of migration, differentiation, and class switching in B cells.}, author = {Kenneth B. Hoehn and Oliver G. Pybus and Steven H. Kleinstein}, year = {2022}, journal = {PLoS Computational Biology}, url = {https://doi.org/10.1371/journal.pcbi.1009885}, doi = {10.1371/journal.pcbi.1009885}, }
@Article{, style = {citation}, title = {Human B cell lineages associated with germinal centers following influenza vaccination are measurably evolving.}, author = {Kenneth B. Hoehn and Jackson S. Turner and Frederick I. Miller and Ruoyi Jiang and Ali H. Ellebedy and Oliver G. Pybus and Steven H. Kleinstein}, year = {2021}, journal = {eLife}, url = {https://elifesciences.org/articles/70873}, doi = {10.7554/eLife.70873}, }
@Article{, style = {citation}, title = {Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination.}, author = {Kenneth B. Hoehn and Jason A. {Van der Heiden} and Julian Q. Zhou and Gerton Lunter and Oliver G. Pybus and Steven H. Kleinstein}, year = {2019}, journal = {PNAS}, url = {https://doi.org/10.1073/pnas.1906020116}, doi = {10.1073/pnas.1906020116}, }
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.