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

MCLeleu 2024-08-13 12:27:13 -04:00
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PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md

@ -11,11 +11,30 @@ For those users interested in eukaryotic phylogeny, we provide a database of 1,0
# Running PhyloToL Part 2 # Running PhyloToL Part 2
Running PhyloToL Part 2 requires at least 4 items in your main directory: 1) A folder named [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL2/Scripts) and containing all scripts from PhyloToL part 2 (**TBD - link to Github?), 2) a folder containing your input files, 3) a taxon list (**TBD - provide example below?) and 4) an OG list (**TBD - provide example below?). Given that PhyloToL part 2 is highly modular and flexible, you will want to be sure of what point to the process of PTLp2 you wish to start and end (**TBD - point to figshare file here -- some figure). The default script starts with raw data and produces trees using scripts 1 - TBD. Running PhyloToL Part 2 requires at least 4 items in your main directory: 1) A folder named [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL2/Scripts) and containing all scripts from PhyloToL part 2, 2) a folder containing your input files, 3) a taxon list and 4) an OG list. Given that PhyloToL part 2 is highly modular and flexible, you will want to be sure of what point to the process of PTLp2 you wish to start and end (**TBD - point to figshare file here -- some figure). The default script starts with raw data and produces trees using scripts 1 - TBD.
The code to run PhyloToL Part 2 in full is 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
>OG6_111062
>OG6_105827
>OG6_107533
>OG6_116087
>OG6_105227
Example of taxon_list.txt
>Am_tu_He65
>EE_cr_Gthe
>Pl_gr_Vaul
>Ba_pa_Mlot
>Op_me_Hsap
>Sr_st_Fves
>Sr_ci_Sx06
>Op_fu_Gzea
>Op_me_Lcha
Modularities Modularities
* If you want to produce trees, you will keep the default '--end’ parameter set to 'trees' * If you want to produce trees, you will keep the default '--end’ parameter set to 'trees'
* If you want to produce up to pre-guidance files, you will change the default '--end’ parameter to 'unaligned' * If you want to produce up to pre-guidance files, you will change the default '--end’ parameter to 'unaligned'