From 333a7bc063aeb7ee8a54f1ae1c60f4e7bed26db0 Mon Sep 17 00:00:00 2001 From: "Godwin N. Ani" Date: Tue, 29 Jul 2025 17:43:37 -0400 Subject: [PATCH] Update run_eukphylo.sh --- PTL2/run_eukphylo.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/PTL2/run_eukphylo.sh b/PTL2/run_eukphylo.sh index fa82cdb..5a4ec6c 100644 --- a/PTL2/run_eukphylo.sh +++ b/PTL2/run_eukphylo.sh @@ -5,6 +5,7 @@ ## the Slurm workload manager. It also includes several example run commands, which correspond to examples explained in more detail in the ## EukPhylo Wiki (https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop). ## These run commands can also be copied and run in the terminal / command line separately, without a shell script. +## For the contamination loop, We recommend iterating the sister/subsisters loop multiple times as branches will shift. In contrast, we recommend only running clade grabbing once ## SLURM-SPECIFIC SETUP BELOW