Merging the rewrite of civet into ARTIC master branch in advance of publication. Stable release of civet 2 exists, and live civet2 branch still available off the artic-network repo.
This version of civet is still in active development, but has a number of generalisations that make it easier to adapt to systems beyond CLIMB-COVID and also for use in other outbreaks.
civet3 no longer requires the presence of a global phylogeny and has optimisations for speed by using an optional SNP file.
Merging the rewrite of civet into ARTIC master branch in advance of publication. Stable release of civet 2 exists, and live civet2 branch still available off the artic-network repo.
This version of civet is still in active development, but has a number of generalisations that make it easier to adapt to systems beyond CLIMB-COVID and also for use in other outbreaks.
civet3 no longer requires the presence of a global phylogeny and has optimisations for speed by using an optional SNP file.