`tree` is used for a developmental lineage. In this form, `tree` should be an `ete3.TreeNode` object representing the root of a Tree with each cell as its leaves. This could be constructed programmatically (see ete3's documentation for details) or if your lineage is stored in a Newick file format, you can load it into an ete3.TreeNode object by running `ete3.Tree('my_newick.txt')`. Note: leaf nodes in the tree must have names that match the column labels in the `counts` input (e.g., cell barcodes).
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