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Updated QuickStart EukPhylo (markdown)

Adri K. Grow 2025-02-03 12:02:08 -05:00
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QuickStart-EukPhylo.md

@ -150,10 +150,10 @@ Below are several optional ways to parameterize EukPhylo Part 2
|`--tree_method`|default = `iqtree`, choices = {`iqtree`, `raxml`, `all`|Change tree building software|
**For BLAST and GUIDANCE:**
|Parameter|Options|Help|
|:---|:---|:---|
|`--blast_cutoff`|default = 1e-20, type = float|Blast e-value cutoff|
|`--len_cutoff`|default = 10, type = int|Amino acid length cutoff for removal of very short sequences after column removal in Guidance|
|Parameter|Options|Description|Default|
|:---|:---|:---|:---|
|`--blast_cutoff`|float|Blast e-value cutoff|`1e-20`
|`--len_cutoff`|default = , type = int|Amino acid length cutoff for removal of very short sequences after column removal in Guidance|10|
|`--guidance_iters`|default = 5, type = int|Number of Guidance iterations for sequence removal|
|`--seq_cutoff`|default = 0.3, type = float|During guidance, taxa are removed if their score is below this cutoff|
|`--col_cutoff`|default = 0.0, type = float|During guidance, columns are removed if their score is below this cutoff|