necom pl

The necom pl module provides integrated pipelines that combine multiple necom operations into a single command.

Currently, only one pipeline is implemented:

• condense: Condense monophyletic subtrees based on a taxonomy TSV file.

For command-line options and usage examples, see docs/help/pl/condense.md.

Full Example with Test Data

necom pl condense --taxon tests/pipeline/strains.taxon.tsv \
    tests/pipeline/minhash.reroot.newick