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Create run_phylotol_command_line.txt

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Example command line to run PhyloToL
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MCLeleu 2024-08-14 10:33:21 -04:00 committed by GitHub
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PTL2/Examplar_runs/Running_PTLp2/run_phylotol_command_line.txt Normal file
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### Download and make your own ReadyToGo_AA_GC3_labelled folder with ReadyToGo files
### Update the taxa list with the taxa files in your ReadyToGo folder
### Download the Script folder
### than run :
python3 Scripts/phylotol.py --start raw --end trees --gf_list list_ogs.txt --taxon_list taxa_list.txt --data ReadyToGo_AA_GC3_labelled --output Output --similarity_filter --sim_cutoff 0.95 --og_identifier OG6 --tree_method iqtree > log1.out