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Updated EukPhylo Part 2: MSAs, trees, and contamination loop (markdown)

Auden Cote-L'Heureux 2025-03-28 15:50:30 -04:00
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EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md

@ -194,7 +194,7 @@ You can also change the tree-building method using the `--cl_tree_method` argume
#### Sisters/subsisters mode #### Sisters/subsisters mode
Below are the parameters for running sisters/subsisters. You must give a rules file to EITHER --sister_rules or --subsister_rules, or both. Below are the parameters for running sisters/subsisters. You must give a rules file to EITHER `--sister_rules` or `--subsister_rules`, or both.
| Parameter | Required | Options | Description | Default | | Parameter | Required | Options | Description | Default |
| ------------- | ------------- | ------------- | ------------- | ------------- | | ------------- | ------------- | ------------- | ------------- | ------------- |