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Updated EukPhylo QuickStart (markdown)

Godwin N. Ani 2025-04-07 15:06:34 -04:00
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EukPhylo-QuickStart.md

@ -223,7 +223,7 @@ Options:
|`--subsister_rules`|only in subsisters mode|Valid path|Path to a text file containing subsisters rules|NA| |`--subsister_rules`|only in subsisters mode|Valid path|Path to a text file containing subsisters rules|NA|
|`--clade_grabbing_rules`|only in clade mode|Valid path|Path to a text file containing clade-grabbing rules|NA| |`--clade_grabbing_rules`|only in clade mode|Valid path|Path to a text file containing clade-grabbing rules|NA|
|`--clade_grabbing_exceptions`|no|Valid path|List of taxa to _not_ remove for any reason|NA| |`--clade_grabbing_exceptions`|no|Valid path|List of taxa to _not_ remove for any reason|NA|
|`--cl_tree_method`|no|`iqtree`, `raxml`, `fasttree`, `iqtree_fast`|Tree-building method to use in each contamination loop iteration|`fasttree`| |`--cl_tree_method`|no|`iqtree`, `raxml`, `fasttree`, `iqtree_fast`|Tree-building method to use in each contamination loop iteration|`iqtree_fast`|
|`--cl_alignment_method`|no|`mafft_only`, `guidance`|Alignment method to use in each contamination loop iteration|`mafft_only`| |`--cl_alignment_method`|no|`mafft_only`, `guidance`|Alignment method to use in each contamination loop iteration|`mafft_only`|
|`--cl_exclude_taxa`|no|Valid path|Path to a file containing taxon names present in input MSA/tree files but which should be removed in the first iteration of the contamination loop|NA| |`--cl_exclude_taxa`|no|Valid path|Path to a file containing taxon names present in input MSA/tree files but which should be removed in the first iteration of the contamination loop|NA|