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Updated EukPhylo QuickStart (markdown)

Adri K. Grow 2025-02-09 01:33:13 -05:00
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EukPhylo-QuickStart.md

@ -148,12 +148,12 @@ Below are several optional ways to parameterize EukPhylo Part 2
|Parameter|Options|Description|Default| |Parameter|Options|Description|Default|
|:---|:---|:---|:---| |:---|:---|:---|:---|
|`--blast_cutoff`|float|Blast e-value cutoff|`1e-20` |`--blast_cutoff`|float|Blast e-value cutoff|`1e-20`
|`--len_cutoff`|int|Amino acid length cutoff for removal of very short sequences after column removal in Guidance|10| |`--len_cutoff`|int|Amino acid length cutoff for removal of very short sequences after column removal in Guidance|`10`|
|`--guidance_iters`|int|Number of Guidance iterations for sequence removal|5| |`--guidance_iters`|int|Number of Guidance iterations for sequence removal|`5`|
|`--seq_cutoff`|float|During guidance, taxa are removed if their score is below this cutoff|0.3| |`--seq_cutoff`|float|During guidance, taxa are removed if their score is below this cutoff|`0.3`|
|`--col_cutoff`|float|During guidance, columns are removed if their score is below this cutoff|0.0| |`--col_cutoff`|float|During guidance, columns are removed if their score is below this cutoff|`0.0`|
|`--res_cutoff`|float|During guidance, residues are removed if their score is below this cutoff|0.0| |`--res_cutoff`|float|During guidance, residues are removed if their score is below this cutoff|`0.0`|
|`--guidance_threads`|int|Number of threads to allocate to Guidance|20| |`--guidance_threads`|int|Number of threads to allocate to Guidance|`20`|
**For reducing number of similar sequences:** **For reducing number of similar sequences:**
|Parameter|Required|Options|Help| |Parameter|Required|Options|Help|