#NEXUS [! Temporary trees from rid3-raxml using the data matrix from data.nex and starting tree from data.nex The following settings were used for the analysis: org.cipres.recidcm3 Parameters: SetTreeDecompModule=*,IDL:CipresIDL_api1/TreeDecompose:1.0,org.cipres.dcm3,Roshan DCM SetLargeTreeInferenceModule=*,IDL:CipresIDL_api1/TreeImprove:1.0,org.cipres.raxml,Python wrapper around RAxMLHPC. file-based io. SetSmallTreeInferenceModule=*,IDL:CipresIDL_api1/TreeImprove:1.0,org.cipres.raxml,Python wrapper around RAxMLHPC. file-based io. SetTreeRefineModule=*,IDL:CipresIDL_api1/TreeRefine:1.0,org.cipres.random-refine,Python implementation of a random refinement of polytomies (Random seed hard-coded for debugging purposes) SetTreeMergeModule=*,IDL:CipresIDL_api1/TreeMerge:1.0,org.cipres.PhycasSCMTreeMerge,C++ implementation of SCM (Yu Fan and Paul Lewis) SetMaxTaxaSubsetPercent=50; SetMaxIterations=10; ignoreStartEdgeLen=no; Tree Decomposer Module Parameters: BreakTies=yes; SEED=0; Large Tree Inference Module Parameters: -c 25 -m GTRGAMMA -i 10 Large Tree Inference Module Parameters: -c 25 -m GTRGAMMA -i 10 ] BEGIN TAXA; Dimensions ntax=12; Taxlabels a b c d e f g u v x y t ; END; BEGIN TREES; Translate 1 a, 2 b, 3 c, 4 d, 5 e, 6 f, 7 g, 8 u, 9 v, 10 x, 11 y, 12 t; [Starting Tree(s)] Tree rep.1[Score=UNSCORED] = [&U]((((1:.1,2:1):1,(12:3.2,7:1):2):1,(3:2,4:1):1):1,(((5:1,6:1):1,8:1):1,9:1.2,(10:0.2,11:1):1):1); [Result Tree(s)] Tree 'Iteration 1 (0h:0m:12s) unnamed_tree_0'[Score=-2157.458839] = [&U](((((11:0.0402134409003,12:0.0703791636747):0.146923115324,3:0.0443434337078):0.00703923641841,2:0.0859973913637):0.00921432465123,(4:0.00862368879072,5:0.0210714051243):0.0601395965455):0.0145309296235,(10:0.0769906500612,(9:0.116025680718,(8:0.03007950279,(6:1.36301333676e-06,7:0.0326414990336):0.0244695578388):0.0480649268473):0.0169463209065):0.0275762098573,1:0.0636886096066):0; Tree 'Iteration 2 (0h:0m:19s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0; Tree 'Iteration 3 (0h:0m:25s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0; Tree 'Iteration 4 (0h:0m:31s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0; Tree 'Iteration 5 (0h:0m:38s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0; Tree 'Iteration 6 (0h:0m:44s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0; Tree 'Iteration 7 (0h:0m:52s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0; Tree 'Iteration 8 (0h:1m:1s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0; Tree 'Iteration 9 (0h:1m:9s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0; Tree 'Iteration 10 (0h:1m:15s) unnamed_tree_0'[Score=-2157.458862] = [&U](((2:0.0859983005494,(3:0.0443436591929,(11:0.0402136791115,12:0.0703788660203):0.146922649123):0.00703895867535):0.00921438056163,(4:0.00862362445331,5:0.0210714657743):0.0601395172569):0.0145311141095,((((6:1.36300496482e-06,7:0.032641561504):0.024469354262,8:0.0300796707656):0.0480650610682,9:0.116025774979):0.0169460328628,10:0.0769905629043):0.0275763279615,1:0.0636887232309):0; [Intermediate Tree(s)] Tree 'Tmp From Iteration 1 '[Score=-2164.911582] = [&U](((((11,12),3),2),(4,5)),(10,(9,(8,(6,7)))),1); Tree 'Tmp From Iteration 1 '[Score=-2164.911582] = [&U](((((11,12),3),2),(4,5)),(10,(9,(8,(6,7)))),1); Tree 'Tmp From Iteration 1 '[Score=-2164.98933] = [&U](((((11,12),3),2),(4,5)),(10,(9,(8,(6,7)))),1); Tree 'Tmp From Iteration 1 '[Score=-2165.072719] = [&U](((((11,12),3),2),(4,5)),(10,(9,(8,(6,7)))),1); Tree 'Tmp From Iteration 1 '[Score=-2165.162458] = [&U](((((11,12),3),2),(4,5)),(10,(9,(8,(6,7)))),1); Tree 'Tmp From Iteration 1 '[Score=-2165.364509] = [&U](((((11,12),3),2),(4,5)),(10,(9,(8,(6,7)))),1); Tree 'Tmp From Iteration 1 '[Score=-2166.3011] = [&U](((((4,5),(11,12)),3),2),(10,(9,(8,(6,7)))),1); Tree 'Tmp From Iteration 2 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 2 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 3 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 3 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 4 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 4 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 5 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 5 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 6 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 6 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 7 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 7 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 8 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 8 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 9 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 9 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 10 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 10 '[Score=-2167.066471] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 2 '[Score=-2167.153167] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 3 '[Score=-2167.153167] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 4 '[Score=-2167.153167] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 5 '[Score=-2167.153167] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 6 '[Score=-2167.153167] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 7 '[Score=-2167.153167] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 8 '[Score=-2167.153167] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 9 '[Score=-2167.153167] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 10 '[Score=-2167.153167] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 2 '[Score=-2167.245639] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 3 '[Score=-2167.245639] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 4 '[Score=-2167.245639] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 5 '[Score=-2167.245639] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 6 '[Score=-2167.245639] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 7 '[Score=-2167.245639] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 8 '[Score=-2167.245639] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 9 '[Score=-2167.245639] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 10 '[Score=-2167.245639] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 2 '[Score=-2168.026584] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 3 '[Score=-2168.026584] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 4 '[Score=-2168.026584] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 5 '[Score=-2168.026584] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 6 '[Score=-2168.026584] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 7 '[Score=-2168.026584] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 8 '[Score=-2168.026584] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 9 '[Score=-2168.026584] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 10 '[Score=-2168.026584] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 2 '[Score=-2170.148838] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 3 '[Score=-2170.148838] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 4 '[Score=-2170.148838] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 5 '[Score=-2170.148838] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 6 '[Score=-2170.148838] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 7 '[Score=-2170.148838] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 8 '[Score=-2170.148838] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 9 '[Score=-2170.148838] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 10 '[Score=-2170.148838] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 2 '[Score=-2177.719768] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 3 '[Score=-2177.719768] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 4 '[Score=-2177.719768] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 5 '[Score=-2177.719768] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 6 '[Score=-2177.719768] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 7 '[Score=-2177.719768] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 8 '[Score=-2177.719768] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 9 '[Score=-2177.719768] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 10 '[Score=-2177.719768] = [&U](((2,(3,(11,12))),(4,5)),((((6,7),8),9),10),1); Tree 'Tmp From Iteration 1 '[Score=-2284.448494] = [&U](2,(((((7,8),6),12),(9,(10,11))),((4,3),5)),1); Tree 'Tmp From Iteration 1 '[Score=-2294.309883] = [&U](2,(((((7,8),6),12),(9,(10,11))),((4,3),5)),1); Tree 'Tmp From Iteration 1 Prior to improvement '[Score=UNSCORED] = [&U](1,2,(((((7,8),6),12),(9,(10,11))),((4,3),5))); Tree 'Tmp From Iteration 2 Prior to improvement '[Score=UNSCORED] = [&U](1,((2,(3,(11,12))),(4,5)),((((6,7),8),9),10)); Tree 'Tmp From Iteration 3 Prior to improvement '[Score=UNSCORED] = [&U](1,((2,(3,(11,12))),(4,5)),((((6,7),8),9),10)); Tree 'Tmp From Iteration 4 Prior to improvement '[Score=UNSCORED] = [&U](1,((2,(3,(11,12))),(4,5)),((((6,7),8),9),10)); Tree 'Tmp From Iteration 5 Prior to improvement '[Score=UNSCORED] = [&U](1,((2,(3,(11,12))),(4,5)),((((6,7),8),9),10)); Tree 'Tmp From Iteration 6 Prior to improvement '[Score=UNSCORED] = [&U](1,((2,(3,(11,12))),(4,5)),((((6,7),8),9),10)); Tree 'Tmp From Iteration 7 Prior to improvement '[Score=UNSCORED] = [&U](1,((2,(3,(11,12))),(4,5)),((((6,7),8),9),10)); Tree 'Tmp From Iteration 8 Prior to improvement '[Score=UNSCORED] = [&U](1,((2,(3,(11,12))),(4,5)),((((6,7),8),9),10)); Tree 'Tmp From Iteration 9 Prior to improvement '[Score=UNSCORED] = [&U](1,((2,(3,(11,12))),(4,5)),((((6,7),8),9),10)); Tree 'Tmp From Iteration 10 Prior to improvement '[Score=UNSCORED] = [&U](1,((2,(3,(11,12))),(4,5)),((((6,7),8),9),10)); END;