File_S5_ContaminationLoop_Process

All files genarated by the Contamination Loop process included in EukPhylo, 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 included
The 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 File S4, 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.