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Updated EukPhylo QuickStart (markdown)

Adri K. Grow 2025-02-09 01:32:29 -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`|default = , type = 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`|default = 5, type = int|Number of Guidance iterations for sequence removal| |`--guidance_iters`|int|Number of Guidance iterations for sequence removal|5|
|`--seq_cutoff`|default = 0.3, type = float|During guidance, taxa are removed if their score is below this cutoff| |`--seq_cutoff`|float|During guidance, taxa are removed if their score is below this cutoff|0.3|
|`--col_cutoff`|default = 0.0, type = float|During guidance, columns are removed if their score is below this cutoff| |`--col_cutoff`|float|During guidance, columns are removed if their score is below this cutoff|0.0|
|`--res_cutoff`|default = 0.0, type = float|During guidance, residues are removed if their score is below this cutoff| |`--res_cutoff`|float|During guidance, residues are removed if their score is below this cutoff|0.0|
|`--guidance_threads`|default = 20, type = int|Number of threads to allocate to Guidance| |`--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|