Appendix_S19_Hoepke_et_al_cpDNA_best.tre 2.65 KB
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#nexus

begin trees;
translate
  1  Plantago_major,
  2  Plantago_rugelii,
  3  Plantago_media,
  4  DCA_1031_P_cafra_South_Africa,
  5  DCA_1406_P_cafra_South_Africa,
  6  DCA_1405_P_cafra_South_Africa,
  7  DCA_1032_P_cafra_South_Africa,
  8  DCA_1402_P_crassifolia_Greece,
  9  AY101952_P_lanceolata_unknown,
  10  DCA_1397_P_maritima_Russia,
  11  DCA_1399_P_subulata_Spain,
  12  DCA_1024_P_crassifolia_South_Africa,
  13  DCA_1025_P_crassifolia_South_Africa,
  14  DCA_1026_P_crassifolia_South_Africa,
  15  DCA_1027_P_crassifolia_South_Africa,
  16  DCA_1029_P_crassifolia_South_Africa,
  17  DCA_1038_P_crassifolia_South_Africa,
  18  DCA_1396_P_crassifolia_South_Africa,
  19  DCA_1033_P_coronopus_South_Africa,
  20  DCA_1424_P_coronopus_Italy,
  21  DCA_1431_P_coronopus_Iran,
  22  DCA_1432_P_coronopus_Spain,
  23  DCA_1433_P_coronopus_Kuwait,
  24  DCA_1438_P_coronopus_Montenegro,
  25  DCA_1390_P_coronopus_Algeria,
  26  DCA_1391_P_coronopus_Algeria,
  27  DCA_1392_P_coronpus_Morocco,
  28  DCA_1395_P_coronopus_Tunisia,
  29  DCA_1097_P_coronopus_Turkey,
  30  DCA_1394_P_coronopus_Spain,
  31  DCA_1036_P_coronopus_South_Africa,
  32  DCA_1407_P_coronopus_Spain,
  33  DCA_1425_P_serraria_Italy,
  34  1470,
  35  1471,
  36  1473,
  37  DCA_1422_P_crypsoides_Saudi_Arabia,
  38  DCA_1403_P_crassifolia_Spain;
tree best = [&U][-3099.7052][ r 1.0467512 1.2137534 0.31570311 0.86648007 1.3557065 b 0.34424491 0.16156708 0.17876248 0.31542553 a 0.19505661 p 0.093571438 ]((4:0.00191184,(7:0.00088507,((((11:0.00501132,10:0.00254702):0.01494626,(((8:0.00000001,38:0.00108582):0.00325449,((23:0.00000001,(21:0.00000001,37:0.00000001):0.00169025):0.00168968,33:0.00178529):0.00000001):0.00982904,((20:0.00096830,(26:0.00000001,((28:0.00083686,((22:0.00000001,(32:0.00000001,(24:0.00000001,(30:0.00000001,27:0.00000001):0.00000001):0.00000001):0.00000001):0.00083477,25:0.00000001):0.00000001):0.00083477,(19:0.00000001,(31:0.00000001,(35:0.00000001,29:0.00000001):0.00000001):0.00000001):0.00083317):0.00000001):0.00000001):0.01015635,(((14:0.00000001,(((18:0.00000001,17:0.00000001):0.00000001,(13:0.00000001,15:0.00000001):0.00000001):0.00000001,16:0.00000001):0.00000001):0.00082588,(12:0.00000001,34:0.00000001):0.00166390):0.00000001,36:0.00165962):0.00183874):0.00160752):0.01098752):0.01625229,(3:0.00449744,(1:0.00253376,2:0.00339983):0.00070965):0.02345332):0.03449014,9:0.01707134):0.00630506):0.00000001):0.00088685,5:0.00000001,6:0.00000001);
end;
begin paup;
clear;
gett file=PlantagocpDNA.best.tre storebr;
lset userbr nst=6 rmat=(1.04675122 1.21375336 0.31570311 0.86648007 1.35570647) base=(0.34424491 0.16156708 0.17876248) rates=gamma shape= 0.19505661 ncat=4 pinv= 0.09357144;
end;