PoonLab/clustuneR: Molecular clustering implementation and predictive optimization

clustuneR builds clusters from inputted sequence alignments and/or phylogenetic trees, allowing users to choose between multiple cluster-building algorithms implememented in the package and tune clustering parameters to produce informative clusters. The package also takes in meta-data associated with sequences such as a known collection date or subtype/variant classification. Cluster-level characteristics, such as the range of collection dates or the most common subtype/variant within a cluster can also be identified from these. If a subset of sequences are specified as "New", then clustuneR simulates cluster growth by building clusters in two stages: first clusters are built from sequences which are not specified as new, then the new sequences are added to clusters. Predictive models can then be tested on cluster-level attributes and validated with growth outcomes, to measure how informative a cluster set is.

install.packages("remotes")
remotes::install_github("PoonLab/clustuneR")