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

Katzlab 2024-08-14 04:57:38 -04:00
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PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md

@ -96,7 +96,7 @@ Adding these options to the command line will give:
`python Scripts/phylotol.py --start raw --end trees --gf_list listofOGs.txt --taxon_list taxon_list.txt --data Input_folder --output Output_folder --similarity_filter --sim_cutoff 0.99 --sim_taxa sim_taxa_list.txt`
###Other optional parameters:
### Other optional parameters:
#### Blacklist
The blacklist is a user-defined set of sequences to be removed from runs. You might choose to keep a list of sequences removed by Guidance to avoid reconsidering these non-homologs in future runs as this can save computer time, if you're going to be using the same ReadyToGo files and GFs in multiple runs of PhyloToL part 2. For our study, we chose to include only sequences removed by Guidance in our blacklist, but users should choose what fits best for their study and their data. To include this parameter in your PhyloToL run, you will need to add the `--blacklist` flag to the command line as follows: