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["Table S1.6.2. Treetrimmer settings"]
[null,"Taxonomic categories to be pruned","Number of OTUs to be retained in each branch"]
["Alveolata","Apicomplexa",2]
["Alveolata","Ciliophora",1]
["Alveolata","Dinophyceae",2]
["Alveolata","Vitrella brassicaformis CCMP3155",1]
["Alveolata","Perkinsus marinus ATCC 50983",1]
["Amoebozoa","Entamoeba",2]
["Amoebozoa","Dictyostelium",1]
["Amoebozoa","Acanthamoeba castellanii str. Neff",1]
["Amoebozoa","Mayorella sp BSH-02190019",1]
["Amoebozoa","Vannella n. sp. DIVA3 517/6/12",1]
["Amoebozoa","Stereomyxa ramosa Chinc5",1]
["Amoebozoa","Trichosphaerium sp Am-I-7 wt",1]
["Amoebozoa","Filamoeba nolandi NC-AS-23-1",1]
["Amoebozoa","Paramoeba pemaquidensis",1000]
["Cryptophyta","Goniomonas sp m",1]
["Cryptophyta","Guillardia theta CCMP2712",1]
["Euglenozoa","Leishmaniinae",2]
["Euglenozoa","Euglena gracilis",1]
["Euglenozoa","Eutreptiella gymnastica NIES-381",1]
["Euglenozoa","Bodo saltans",1]
["Euglenozoa","Neobodo designis CCAP 1951/1",1]
["Euglenozoa","Phytomonas sp. isolate EM1",1]
["Euglenozoa","Trypanosoma brucei brucei strain 927/4 GUTat10.1",1]
["Euglenozoa","Trypanosoma cruzi strain CL Brener",1]
["Euglenozoa","Diplonema papillatum",1]
["Euglenozoa","Perkinsela sp.",1000]
["Fornicata","Giardia lamblia ATCC 50803",1]
["Glaucocystophyceae","Glaucocystophyceae",1]
["Haptophyceae","Isochrysis aff. galbana",1]
["Haptophyceae","Emiliania huxleyi CCMP1516",1]
["Haptophyceae","Pavlovales sp. CCMP2436",1]
["Heterolobosea","Naegleria gruberi",1]
["Katablepharidophyta","Roombia truncata",1]
["Opisthokonta","Fungi",2]
["Opisthokonta","Metazoa",2]
["Opisthokonta","Monosiga brevicollis MX1",1]
["Opisthokonta","Salpingoeca rosetta",1]
["Parabasalia","Trichomonas vaginalis G3",1]
["Rhizaria","Phyllostaurus sp.",1]
["Rhizaria","Astrolonche sp.",1]
["Rhizaria","Bigelowiella natans CCMP2755",1]
["Rhizaria","Limnofila sp. \"Gymnophrys\"",1]
["Rhizaria","Plasmodiophora brassicae",1]
["Rhizaria","Spongospora subterranea",1]
["Rhizaria","Quinqueloculina sp.",1]
["Rhizaria","Reticulomyxa filosa",1]
["Rhizaria","Gromia sphaerica",1]
["Rhizaria","Corallomyxa tenera",1]
["Rhodophyta","Rhodophyta",2]
["Stramenopiles","Bacillariophyta",1]
["Stramenopiles","Blastocystis hominis",1]
["Stramenopiles","Nannochloropsis gaditana CCMP526",1]
["Stramenopiles","Phytophthora infestans T30-4",1]
["Stramenopiles","Aureococcus anophagefferens",1]
["Stramenopiles","Ectocarpus siliculosus",1]
["Viridiplantae","Streptophyta",1]
["Viridiplantae","Chlorophyceae",1]
["Viridiplantae","Mamiellophyceae",1]
["Viridiplantae","Trebouxiophyceae",1]
["Archaea","Euryarchaeota",1]
["Archaea","Thaumarchaeota",1]
["Bacteria","Bacteria",2]