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Updated EukPhylo QuickStart (markdown)

MCLeleu 2025-04-29 11:18:22 +02:00
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EukPhylo-QuickStart.md

@ -194,7 +194,7 @@ Below are several optional ways to parameterize EukPhylo Part 2
|`--og_identifier`|`OG`, `OG6`, `OGA`, `OGG`|Select sequences by GC width|`OG` |`--og_identifier`|`OG`, `OG6`, `OGA`, `OGG`|Select sequences by GC width|`OG`
## Contamination Removal ## Contamination Removal
Contamination removal within EukPhylo (also called Contamination Loop or CL) allows for sequence removal based on Sisters/Subsisters identification or based on Clades diversity. An examplar run is available in [Figshare](https://figshare.com/articles/dataset/Examplar_runs_PhyloToL_and_CLoop/26662018) Contamination removal within EukPhylo (also called Contamination Loop or CL) allows for sequence removal based on Sisters/Subsisters identification or based on Clades diversity. An examplar run is available in [Figshare](https://figshare.com/projects/EukPhylo_Supplemental_Files/196552)
### Set up: ### Set up:
* An input folder (called for example Input), with both * An input folder (called for example Input), with both