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

MCLeleu 2024-08-13 13:17:43 -04:00
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PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md

@ -17,22 +17,22 @@ The code to run PhyloToL Part 2 in full is
> python Scripts/phylotol.py --start raw --end trees --gf_list listofOGs.txt --taxon_list taxon_list.txt --data Input_folder --output Output_folder > Output1.out > python Scripts/phylotol.py --start raw --end trees --gf_list listofOGs.txt --taxon_list taxon_list.txt --data Input_folder --output Output_folder > Output1.out
Example of listofOGs.txt Example of listofOGs.txt
>OG6_111062 OG6_111062
OG6_105827 OG6_105827
>OG6_107533 OG6_107533
>OG6_116087 OG6_116087
>OG6_105227 OG6_105227
Example of taxon_list.txt Example of taxon_list.txt
>Am_tu_He65 Am_tu_He65
>EE_cr_Gthe EE_cr_Gthe
>Pl_gr_Vaul Pl_gr_Vaul
>Ba_pa_Mlot Ba_pa_Mlot
>Op_me_Hsap Op_me_Hsap
>Sr_st_Fves Sr_st_Fves
>Sr_ci_Sx06 Sr_ci_Sx06
>Op_fu_Gzea Op_fu_Gzea
>Op_me_Lcha Op_me_Lcha
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