diff --git a/PhyloToL-Part-2.md b/PhyloToL-Part-2.md index 0c21a96..ed9b2db 100644 --- a/PhyloToL-Part-2.md +++ b/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_ +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 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: