diff --git a/QuickStart-EukPhylo.md b/QuickStart-EukPhylo.md index 5a74567..d2664b1 100644 --- a/QuickStart-EukPhylo.md +++ b/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|