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Godwin N. Ani 2025-07-29 17:43:37 -04:00 committed by GitHub
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## the Slurm workload manager. It also includes several example run commands, which correspond to examples explained in more detail in the ## 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). ## 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. ## 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 ## SLURM-SPECIFIC SETUP BELOW