Main tool: transcluster
Code repository: https://github.com/JamesStimson/transcluster
Basic information on how to use this tool:
- executable:
R - help:
help(package='transcluster') - version:
help(package='transcluster') - description: transcluster is an R package for inferring and viewing transmission clusters from sequence alignments and sample dates.
Additional information:
ContaStimson, J., Gardy, J., Barun Mathema, Valeriu Crudu, Cohen, T., & Colijn, C. (2018). Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions. Molecular Biology and Evolution, 36(3), 587–603. https://doi.org/10.1093/molbev/msy242
Full documentation: Further information is available in the following vignettes in directory /usr/local/lib/R/site-library/transcluster/doc
Example scripts:
R < my_script.R ['--save', '--no-save' or '--vanilla']