Dataset_S19_ContaminationLoop_Process

All files genarated by the Contamination Loop process included in PhyloToL6, for 500 GF on a 1000 taxa. This include 1. Sisters contamination removal, 2. Subsisters contamination removal, 3. Ciliates Clade Grabbing, 4. Clade Grabbing and 5. EGT identification.For all steps, Alignements, Trees, Colored Trees (both by Major Clades and By Sequences removed by the CLoop steps) and a list a sequences removed are includedThe output of the contamination loop in PhyloToL part 2 at each step of the process (sisters-based removal, subsisters-based removal, clade grabbing of ciliates, general clade grabbing, and EGT removal) in the analysis of 500 OGs across 1000 taxa. Each folder contains all outputs described for the pre-contamination files in the legend for Dataset S18, as well as a record of all the sequences removed by that contamination loop step (SequencesRemoved_ContaminationLoop.txt) and a folder of the trees input to that step with all removed sequences colored grey. The EGT removal step includes also the trees identified as containing primary and secondary endosymbiosis.