diff --git a/EukPhylo-QuickStart.md b/EukPhylo-QuickStart.md index be57d17..0646f33 100644 --- a/EukPhylo-QuickStart.md +++ b/EukPhylo-QuickStart.md @@ -148,12 +148,12 @@ Below are several optional ways to parameterize EukPhylo Part 2 |Parameter|Options|Description|Default| |:---|:---|:---|:---| |`--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| -|`--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| -|`--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| -|`--guidance_threads`|int|Number of threads to allocate to Guidance|20| +|`--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`| +|`--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`| +|`--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`| **For reducing number of similar sequences:** |Parameter|Required|Options|Help|