prune_tree_by_tid

DatabaseGreengenes.prune_tree_by_tid(ids, subreps=False, include_rid=False)

Prune reference tree and keep tips with ids

Parameters

  • ids (Union[Sequence[Union[str, int]], numpy.ndarray, pandas.core.indexes.base.Index, str, int]) – Target tids or tips of the tree to keep.

  • subreps (bool) – Whether to look for subs.

  • include_rid (bool) – Whether to keep phylogeny with rids attached to tids.

Returns

Return type

Pruned reference phylogenetic tree.