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Updated EukPhylo Part 2: MSAs, trees, and contamination loop (markdown)

GiuliaRibeiro 2025-04-18 13:17:23 -04:00
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EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md

@ -141,6 +141,8 @@ Argument | Default | Choices | Description
-- | -- | -- | -- -- | -- | -- | --
--tree_method | iqtree_fast | iqtree, iqtree_fast, raxml, fasttree | Program to use for tree-building. --tree_method | iqtree_fast | iqtree, iqtree_fast, raxml, fasttree | Program to use for tree-building.
NOTE: These processes are resource-intensive. Each system has its own syntax and requirements for running resource-intensive jobs. Here, we added examples of how we run in our local Smith College 'grid' system and on the more powerful HPC Unity cluster. Please adjust the 'tree.py' and 'run_eukphylo.sh' scripts to match with your system's capabilities, as specified in the scripts.
## Contamination loop ## Contamination loop
The contamination coop (CL) is implemented within EukPhylo to allow the removal of contaminants based on the topology of each tree (phylogeny-informed contamination removal). Three modes are available: sister-, subsister-, and clade-based contamination removal. All modes take a user defined file of 'rules,' used to identify the sequences to remove. We first provide an overview of the three modes and then give details on running below. The contamination coop (CL) is implemented within EukPhylo to allow the removal of contaminants based on the topology of each tree (phylogeny-informed contamination removal). Three modes are available: sister-, subsister-, and clade-based contamination removal. All modes take a user defined file of 'rules,' used to identify the sequences to remove. We first provide an overview of the three modes and then give details on running below.