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Updated PhyloToL Part 2 (markdown)

Katzlab 2024-08-09 18:12:16 -04:00
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PhyloToL-Part-2.md

@ -20,7 +20,7 @@ Clade-based contamination removal operates differently. In this mode, the CL sea
The CL runs iteratively, _meaning_... The CL runs iteratively, _meaning_...
## Setup ## Contamination loop setup
The CL requires 1) a folder of alignments (not gap trimmed) and 2) a folder of gene trees in order to run, and they should be formatted in the same way as output by the preceding steps of PhyloToL part 2 (i.e. in the "Output" folder, see above). You can also give it data _not_ output by PhyloToL, but you will need to match the folder, file, and sequence name formats. The CL requires 1) a folder of alignments (not gap trimmed) and 2) a folder of gene trees in order to run, and they should be formatted in the same way as output by the preceding steps of PhyloToL part 2 (i.e. in the "Output" folder, see above). You can also give it data _not_ output by PhyloToL, but you will need to match the folder, file, and sequence name formats.