ALPPACA is a pipeline for various phylogenetic analyses of prokaryotic isolates. The pipeline includes core genome-, core gene-, and reference-based (mapping) phylogeny, as well as FastANI and cgMLST (under development). Please see the description page for more information.
Please check the wiki.
ALPPACA has been published in Journal of Open Source Software. Use the following citation:
Kaspersen et al., (2022). ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis. Journal of Open Source Software, 7(79), 4677, https://doi.org/10.21105/joss.04677