From 44b854661205f9854b71090f3f83d9054e43c189 Mon Sep 17 00:00:00 2001 From: Katzlab Date: Fri, 9 Aug 2024 17:40:09 -0400 Subject: [PATCH] Updated PhyloToL Part 2 (markdown) --- PhyloToL-Part-2.md | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/PhyloToL-Part-2.md b/PhyloToL-Part-2.md index 34b4429..8349018 100644 --- a/PhyloToL-Part-2.md +++ b/PhyloToL-Part-2.md @@ -18,20 +18,26 @@ Sisters-based contamination removal identifies sequences as putative contaminant Clade-based contamination removal operates differently. In this mode, the CL searches for monophyletic clades in each gene tree that match a set of given criteria. For example, if we want to 'clade-grab' for robust Opisthokont clades, we might choose to keep only Opisthokont sequences that fall in a monophyletic clade of 12 or more species of Opisthokont; all other Opisthokont sequences in the tree would be removed. +The CL runs iteratively, _meaning_... + ## 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. You will also need to create a 'rules' file. The format here varies between the different modes of the CL. +_describe rules files here_ + ## 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: -| Parameter | required | Options | Description | default | +| Parameter | Required | Options | Description | Default | | ------------- | ------------- | ------------- | ------------- | ------------- | -| --contamination_loop | yes | seq, clade | The mode in which to run the loop | none | +| --contamination_loop | yes | seq, clade | The mode in which to run the CL | none | | --nloops | no | _int_ | Number of iterations | 5 | +| --sister_rules | in sisters mode | Path to a file | Sisters rules file | none | +| --subsister_rules | in subsisters mode | Path to a file | Subsisters rules file | none |