Appendix_S6_Hoepke_et_al_ITS_best.tre 5.15 KB
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#nexus

begin trees;
translate
  1  Plantago_uniflora,
  2  Plantago_rigida_new_48,
  3  Plantago_major,
  4  Plantago_camtschatica,
  5  Plantago_rugelii,
  6  Plantago_media,
  7  Plantago_stauntonii,
  8  Plantago_amplexicaulis,
  9  Plantago_webbii,
  10  Plantago_mauretanica,
  11  Plantago_arenaria,
  12  Plantago_afra,
  13  Plantago_brasiliensis,
  14  Plantago_erecta,
  15  Plantago_aristata,
  16  Plantago_patagonica,
  17  Plantago_cretica,
  18  Plantago_lagopus,
  19  AY101895_P_atrata_Kaukasus,
  20  DCA_1031_P_cafra_South_Africa,
  21  DCA_1406_P_cafra_South_Africa,
  22  DCA_1405_P_cafra_South_Africa,
  23  DCA_1032_P_cafra_South_Africa,
  24  AY101896_P_nivalis_Spain,
  25  AY101898_P_lanceolata_unknown,
  26  AY101877_P_alpina_unknown,
  27  AY101879_P_maritima_unknown,
  28  HQ593837_P_maritima_unknown,
  29  DCA_1397_P_maritima_Russia,
  30  AY101878_P_subulata_unknown,
  31  DCA_1399_P_subulata_Spain,
  32  DCA_1024_P_crassifolia_South_Africa,
  33  DCA_1025_P_crassifolia_South_Africa,
  34  DCA_1026_P_crassifolia_South_Africa,
  35  DCA_1027_P_crassifolia_South_Africa,
  36  DCA_1029_P_crassifolia_South_Africa,
  37  DCA_1030_P_crassifolia_South_Africa,
  38  DCA_1038_P_crassifolia_South_Africa,
  39  DCA_1396_P_crassifolia_South_Arica,
  40  AF515217_P_coronopus_England,
  41  DCA_1403_P_crassifolia_Spain,
  42  AY101881_P_crassifolia_unknown,
  43  DCA_1413_P_coronopus_South_Africa,
  44  DCA_1033_P_coronopus_South_Africa,
  45  AY101882_P_coronopus_Denmark,
  46  HQ593830_P_coronopus_unknown,
  47  HQ593832_P_coronopus_unknown,
  48  HQ593833_P_coronopus_unknown,
  49  DCA_1424_P_coronopus_Italy,
  50  DCA_1430_P_coronopus_Malta,
  51  DCA_1431_P_coronopus_Iran,
  52  DCA_1432_P_coronopus_Spain,
  53  DCA_1433_P_coronopus_Kuwait,
  54  DCA_1436_P_coronopus_Bahrain,
  55  DCA_1438_P_coronopus_Montenegro,
  56  DCA_1443_P_coronopus_Saudi_Arabia,
  57  DCA_1390_P_coronopus_Algeria,
  58  DCA_1391_P_coronopus_Algeria,
  59  DCA_1392_P_coronopus_Morocco,
  60  DCA_1395_P_coronopus_Tunisia,
  61  DCA_1097_P_coronopus_Turkey,
  62  DCA_1394_P_coronopus_Spain,
  63  DCA_1036_P_coronopus_South_Africa,
  64  DCA_1407_P_coronopus_Spain,
  65  HQ593835_P_macrorhiza_unknown,
  66  HQ593834_P_macrorhiza_unknown,
  67  AY101883_P_macrorhiza_unknown,
  68  AY101880_P_serraria_unknown,
  69  DCA_1425_P_serraria_Italy,
  70  AY101884_P_subspathulata_Portugal,
  71  1470,
  72  1471,
  73  1473,
  74  DCA_1408_P_coronopus_South_Africa,
  75  DCA_1444_P_coronopus_Iran,
  76  KF815505_P_coronopus_Saudi_Arabia,
  77  DCA_1440_P_coronopus_Portugal,
  78  DCA_1441_P_coronopus_Portugal,
  79  DCA_1401_P_crassifolia_Spain,
  80  DCA_1402_P_crassifolia_Greece,
  81  DCA_1037_P_crassifolia_South_Africa,
  82  1472;
tree best = [&U][-3959.23][ r 0.82334852 1.225638 1.0779893 0.25574692 3.6255638 b 0.25 0.25 0.25 0.25 a 0.74684903 p 0.40820751 ](32:0.00000001,(37:0.00313094,((36:0.00469025,(38:0.00000001,(35:0.00000001,((39:0.00312954,33:0.00000001):0.00154945,73:0.00000001):0.00000001):0.00000001):0.00000001):0.00467542,((81:0.00625494,(82:0.00317049,((((80:0.00154122,(41:0.00000001,79:0.00000001):0.00000001):0.00547905,(42:0.00389786,((54:0.00000001,51:0.00000001):0.00469239,(53:0.00153990,56:0.00000001):0.00000001):0.00864412):0.00156886):0.00226405,((68:0.00159015,((((((29:0.00655821,31:0.00187707):0.00160320,30:0.00522482):0.00269549,26:0.00324537):0.00529569,28:0.00488710):0.00000001,27:0.00000001):0.04320364,(((8:0.04184749,(((12:0.00995177,11:0.03640117):0.00549402,(9:0.01482691,10:0.00529008):0.00489715):0.02351676,((13:0.01134686,(14:0.00336167,(15:0.00596829,16:0.00763046):0.00881204):0.00342921):0.02606170,17:0.01821860):0.02940580):0.01050258):0.00555149,(((24:0.00955012,19:0.00459112):0.00219757,((20:0.00000001,23:0.00150972):0.00151921,(21:0.00000001,22:0.00000001):0.00000001):0.01529952):0.01545982,(25:0.00091508,18:0.01631479):0.02803970):0.00944842):0.01162594,(((3:0.00342406,2:0.03361187):0.00309956,((7:0.01995744,(4:0.01294451,5:0.01626633):0.00587683):0.00301872,6:0.01966945):0.00187264):0.07042339,1:0.05790742):0.00692353):0.05208051):0.01081098):0.00158062,(69:0.00000001,50:0.00000001):0.00310465):0.00155214):0.00798110,((((61:0.00321615,((43:0.00000001,(((72:0.00000001,(74:0.00000001,44:0.00000001):0.00153312):0.00153552,63:0.00000001):0.00000001,76:0.00316446):0.00000001):0.00000001,75:0.00000001):0.00155270):0.00000001,((((60:0.00000001,65:0.00000001):0.00000001,67:0.00000001):0.00000001,66:0.00000001):0.00153707,((55:0.00000001,(46:0.00000001,(52:0.00152742,47:0.00000001):0.00000015):0.00000001):0.00000001,((40:0.00000001,78:0.00000001):0.00000001,(((62:0.00000001,77:0.00000001):0.00000001,57:0.00000001):0.00000001,(48:0.00000001,(45:0.00000001,64:0.00000001):0.00000001):0.00000001):0.00000001):0.00000001):0.00153960):0.00152353):0.00152986,(70:0.00152817,59:0.00000001):0.00000001):0.00476510,(49:0.00000001,58:0.00000001):0.00142328):0.01836451):0.00318171):0.00000001):0.00156525,34:0.00950178):0.00000148):0.00000001):0.00311078,71:0.00163095);
end;
begin paup;
clear;
gett file=PlantagoITS.best.tre storebr;
lset userbr nst=6 rmat=(0.82334852 1.22563799 1.07798929 0.25574692 3.62556384) base=eq  rates=gamma shape= 0.74684903 ncat=4 pinv= 0.40820751;
end;