added output files

make_phylogeny/aligned.tre

@@ -0,0 +1 @@
+(((((New.0.ReferenceOTU54:0.35879,(r178:0.324724,New.0.CleanUp.ReferenceOTU17:0.305197):0.037218):0.013536,r192:0.349891):0.013985,((((r70:0.323771,(r74:0.159482,New.0.ReferenceOTU13:0.159667):0.162338):0.158415,(New.0.ReferenceOTU9:0.34701,r28:0.401266):0.013522):0.024153,(r0:0.480973,r143:0.497885):0.037235):0.024544,New.0.ReferenceOTU15:0.394723):0.025819):0.026368,((((((((((r181:0.182564,r59:0.187086):0.026451,(New.0.ReferenceOTU30:0.221519,New.0.CleanUp.ReferenceOTU29:0.230588):0.007737):0.007147,New.0.ReferenceOTU52:0.233584):0.02359,(New.0.CleanUp.ReferenceOTU33:0.246002,(New.0.ReferenceOTU32:0.207296,New.0.ReferenceOTU7:0.201434):0.050436):0.022108):0.043211,New.0.ReferenceOTU14:0.308822):0.015695,(New.0.ReferenceOTU17:0.198784,New.0.ReferenceOTU28:0.177156):0.146924):0.029292,(New.0.ReferenceOTU38:0.380089,New.0.ReferenceOTU49:0.353953):0.012534):0.015233,((New.0.ReferenceOTU57:0.291168,r84:0.315728):0.051689,r162:0.355406):0.028696):0.005469,((((r102:0.30589,(r111:0.258003,New.0.CleanUp.ReferenceOTU19:0.24533):0.04504):0.030236,r175:0.328116):0.034689,((r146:0.300305,r153:0.312477):0.029548,(((New.0.ReferenceOTU48:0.136765,New.0.CleanUp.ReferenceOTU7:0.146103):0.152397,New.0.ReferenceOTU29:0.308912):0.011931,(r39:0.294181,r63:0.268319):0.032907):0.013369):0.016664):0.00967,(((New.0.ReferenceOTU51:0.279763,New.0.ReferenceOTU36:0.291666):0.012029,r78:0.291684):0.036915,((((New.0.ReferenceOTU22:0.26403,New.0.ReferenceOTU34:0.23597):0.04863,(((New.0.ReferenceOTU39:0.156736,r129:0.135754):0.054909,New.0.ReferenceOTU33:0.189838):0.06294,New.0.ReferenceOTU5:0.2311):0.052574):0.002956,(((r148:0.143675,New.0.CleanUp.ReferenceOTU9:0.147512):0.119739,r47:0.254713):0.051694,(New.0.ReferenceOTU26:0.229361,New.0.ReferenceOTU42:0.211072):0.071532):0.003936):0.025679,r158:0.326848):0.007208):0.011598):0.009777):0.007267,(r49:0.336327,New.0.CleanUp.ReferenceOTU12:0.353568):0.032916):0.008052),(New.0.ReferenceOTU6:0.420765,(New.0.ReferenceOTU41:0.379228,((r38:0.281275,r92:0.270056):0.026713,r96:0.317539):0.047547):0.019802):0.007315);

make_phylogeny/rep_phylo.tre

@@ -0,0 +1 @@
+(((((((New.0.ReferenceOTU5:0.05067,(New.0.ReferenceOTU33:0.10526,(New.0.ReferenceOTU39:0.00016,r129:0.04665)0.993:0.09542)0.988:0.14134)0.978:0.13902,(New.0.ReferenceOTU36:0.12367,((r148:0.16175,New.0.CleanUp.ReferenceOTU9:0.00016)0.999:0.17786,r47:0.023)0.779:0.07434)0.993:0.14975)0.907:0.09058,(r78:0.26492,(New.0.ReferenceOTU22:0.11636,New.0.ReferenceOTU34:0.04549)0.703:0.01733)0.880:0.05224)0.832:0.08021,New.0.ReferenceOTU51:0.14487)0.433:0.02668,(New.0.ReferenceOTU26:0.03188,New.0.ReferenceOTU42:0.21485)0.341:0.01962)0.371:0.08711,r28:0.63554)0.650:0.03085,((r158:0.19778,(r96:0.12601,(r38:0.24145,r92:0.297)0.943:0.16926)0.999:0.19538)0.892:0.12716,(r146:0.26593,((((r181:0.15944,((New.0.ReferenceOTU32:0.06939,((New.0.CleanUp.ReferenceOTU33:0.23266,New.0.CleanUp.ReferenceOTU29:0.067)0.209:0.05032,New.0.ReferenceOTU14:0.39581)0.817:0.04969)0.897:0.07762,((New.0.ReferenceOTU7:0.07948,r59:0.04644)0.627:0.02639,(New.0.ReferenceOTU17:0.16137,New.0.ReferenceOTU28:0.04686)0.999:0.17798)0.944:0.08501)0.400:0.02682)0.089:0.00611,((New.0.ReferenceOTU30:0.11078,New.0.ReferenceOTU52:0.06277)0.497:0.03057,(((((r70:0.3363,(r0:0.00116,r143:1.2314)0.081:0.50764)0.425:0.15912,New.0.ReferenceOTU49:0.00016)0.855:0.09762,New.0.ReferenceOTU13:0.04006)0.255:0.01316,r74:0.20638)0.999:0.4103,New.0.ReferenceOTU38:0.54196)0.000:0.00016)0.260:0.05949)0.831:0.14971,(New.0.ReferenceOTU57:0.25477,r84:0.10524)0.998:0.40986)0.959:0.21713,(((New.0.ReferenceOTU48:0.09656,New.0.CleanUp.ReferenceOTU7:0.03314)0.989:0.20998,(r153:0.2175,((r102:0.0974,r175:0.40572)0.964:0.2358,(New.0.CleanUp.ReferenceOTU19:0.17636,r111:0.07083)0.841:0.14281)0.591:0.20414)0.373:0.15365)0.823:0.09797,(New.0.ReferenceOTU29:0.28773,(r39:0.19166,r63:0.12122)0.878:0.08664)0.744:0.06053)0.781:0.07918)0.915:0.14771)0.629:0.05893)0.749:0.05953,((New.0.ReferenceOTU15:0.36885,(New.0.ReferenceOTU41:0.4242,r192:0.06058)0.764:0.09601)0.809:0.10529,(New.0.ReferenceOTU9:0.22154,(((r162:0.45819,(New.0.CleanUp.ReferenceOTU12:0.44102,New.0.ReferenceOTU6:0.75725)0.299:0.1103)0.089:0.00015,r49:0.17029)0.973:0.22038,(New.0.ReferenceOTU54:0.18481,(New.0.CleanUp.ReferenceOTU17:0.16433,r178:0.48934)0.949:0.23612)0.807:0.16454)0.478:0.02748)0.230:0.11348)0.966:0.16346);