Tools

zombi2 tools reads a finished run and derives a new view of it. Each tool is a sub-subcommand, zombi2 tools <tool>. format reads a whole genomes run and writes its derived files beside the run; tree and treedist read one or two Newick files and write to stdout, or to a file with -o. compact and expand convert a written run from the per-family layout to the compact layout, or back.

• format — analysis-ready files from a genomes run
• tree — one transform on a Newick tree
• treedist — distance between two trees
• compact and expand — compact files or per-family files