File_S4_PreContaminationLoop_Alignments_Trees

Dataset produced by EukPhylo part 2, before any removal by the Contamination Loop. Include Alignments and Trees and all steps of the pipeline for 500 GF and 1000 taxa.All alignments and trees before phylogeny-informed contamination removal (running), as output by EukPhylo part 2 for the analysis of 500 OGs across 1000 taxa. Files in the folder PreGuidance are the result of the initial file reorganization (to group sequences by OG and apply overlap/similarity filters). The folder NotGapTrimmed contains the MSAs output by Guidance, with putative non-homologs removed, and the folder Guidance contains the same MSAs gap trimmed at 95% gaps. The folder Trees has the raw output, and renamed and colored versions are also given