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Updated PhyloToL Part 2 (markdown)

Katzlab 2024-08-09 17:50:12 -04:00
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PhyloToL-Part-2.md

@ -28,6 +28,14 @@ You will also need to create a 'rules' file. The format here varies between the
_describe rules files here_ _describe rules files here_
Having well-organized ten-digit-codes for sample identification is vital for running the CL, especially clade grabbing, because it will allow the CL to find all sequences belonging to taxa from a specific taxonomic group. For example, in the ten-digit-codes used in the 1000-ReadyToGo file database, in order to clade grab for Opisthokonta the CL will look for all sequences with ten-digit-codes starting with `Op_`, and to clade grab for Metazoa, all ten-digit-codes starting with `Op_me`, etc.
The columns in the rules file are
| Column | Input options | Description |
| ------------- | ------------- | ------------- | ------------- | ------------- |
| Target taxa |
## Running ## Running
To run the CL, use a similar command structure as described for running PhyloToL part 2 above, and add the `--contamination_loop` parameter to activate the contamination loop and specify a mode and the path to a rules file. Available parameters are: To run the CL, use a similar command structure as described for running PhyloToL part 2 above, and add the `--contamination_loop` parameter to activate the contamination loop and specify a mode and the path to a rules file. Available parameters are: