Appendix_S20_Hoepke_et_al_cpDNA_garli_consensus.tre 17.7 KB
Newer Older
Jannes Höpke's avatar
Jannes Höpke committed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
#NEXUS

[
=============
Summary Trees
=============

Summary trees generated by SumTrees.

Summarization Information
-------------------------
Trees read from 1 source(s):
- 'PlantagocpDNA.boot.tre'
Total of 1000 trees analyzed for summarization:
- All trees were treated as unweighted
- All trees were unrooted
- 38 unique taxa across all trees
- 1548 unique splits out of a total of 74000 splits
- 1509 unique non-trivial splits counted out of a total of non-trivial 35000 splits
Summarized onto consensus tree with minimum clade frequency threshold of 0.5:
- Target tree(s) rotated to set outgroup: 'Plantago rugelii'
- Support values expressed as percentages
- Edge lengths on target trees set to mean of edge lengths in sources
- Support and other summarization annotations added to target trees as metadata

Program Information
-------------------
SumTrees 4.0.0 (Jan 31 2015) by Jeet Sukumaran and Mark T. Holder
Using None, located at: '/home/jannes/Additional_applications/miniconda2/envs/py3-sumtrees/lib/python3.4/site-packages/DendroPy-4.0.3-py3.4.egg/dendropy'
Running under Python 3.4.5 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:47:47) (GCC 4.4.7 20120313 (Red Hat 4.4.7-1)), located at: '/home/jannes/Additional_applications/miniconda2/envs/py3-sumtrees/bin/python'

Execution Information
---------------------
Executed on jannes-pc by jannes@jannes-pc
Working directory: '/home/jannes/Desktop/Plantago'
Started at: 2019-02-25 14:41:06.946229
Ended at: 2019-02-25 14:41:11.519353
Total elapsed time: 4.573124 seconds
Actual analysis time: 4.486025 seconds

Citation Information
--------------------

  Sukumaran, J and MT Holder. 2010. DendroPy: a Python library for
    phylogenetic computing. Bioinformatics 26: 1569-1571.

  Sukumaran, J and MT Holder. SumTrees: Phylogenetic Tree
    Summarization. 4.0.0 (Jan 31 2015). Available at
    https://github.com/jeetsukumaran/DendroPy.

]
BEGIN TAXA;
    DIMENSIONS NTAX=38;
    TAXLABELS
        Plantago_major
        Plantago_rugelii
        Plantago_media
        DCA_1031_P_cafra_South_Africa
        DCA_1406_P_cafra_South_Africa
        DCA_1405_P_cafra_South_Africa
        DCA_1032_P_cafra_South_Africa
        DCA_1402_P_crassifolia_Greece
        AY101952_P_lanceolata_unknown
        DCA_1397_P_maritima_Russia
        DCA_1399_P_subulata_Spain
        DCA_1024_P_crassifolia_South_Africa
        DCA_1025_P_crassifolia_South_Africa
        DCA_1026_P_crassifolia_South_Africa
        DCA_1027_P_crassifolia_South_Africa
        DCA_1029_P_crassifolia_South_Africa
        DCA_1038_P_crassifolia_South_Africa
        DCA_1396_P_crassifolia_South_Africa
        DCA_1033_P_coronopus_South_Africa
        DCA_1424_P_coronopus_Italy
        DCA_1431_P_coronopus_Iran
        DCA_1432_P_coronopus_Spain
        DCA_1433_P_coronopus_Kuwait
        DCA_1438_P_coronopus_Montenegro
        DCA_1390_P_coronopus_Algeria
        DCA_1391_P_coronopus_Algeria
        DCA_1392_P_coronpus_Morocco
        DCA_1395_P_coronopus_Tunisia
        DCA_1097_P_coronopus_Turkey
        DCA_1394_P_coronopus_Spain
        DCA_1036_P_coronopus_South_Africa
        DCA_1407_P_coronopus_Spain
        DCA_1425_P_serraria_Italy
        1470
        1471
        1473
        DCA_1422_P_crypsoides_Saudi_Arabia
        DCA_1403_P_crassifolia_Spain
  ;
END;

BEGIN TREES;
    TREE 1 = [&U] (Plantago_rugelii:0.0034375359299999974[&support=100.0][&length_mean=0.0034375359299999974,length_median=0.0033793499999999997,length_sd=0.0017499165259608166,length_hpd95={0.000805,0.0070028},length_quant_5_95={0.00083565,0.00675398},length_range={1e-08,0.00950592}],(Plantago_media:0.00426001299[&support=100.0][&length_mean=0.00426001299,length_median=0.0041651299999999995,length_sd=0.0021951196257727758,length_hpd95={0.00084313,0.00882744},length_quant_5_95={0.00101041,0.00818242},length_range={1e-08,0.01408252}],((AY101952_P_lanceolata_unknown:0.01738485560000002[&support=100.0][&length_mean=0.01738485560000002,length_median=0.017134045,length_sd=0.005009188358224625,length_hpd95={0.00773687,0.02697266},length_quant_5_95={0.00966188,0.0258357},length_range={0.00228791,0.03807121}],(DCA_1031_P_cafra_South_Africa:0.0018325833199999998[&support=100.0][&length_mean=0.0018325833199999998,length_median=0.001866915,length_sd=0.0013774993022419486,length_hpd95={1e-08,0.004176},length_quant_5_95={1e-08,0.0041298},length_range={1e-08,0.0091111}],DCA_1032_P_cafra_South_Africa:0.0005879062900000014[&support=100.0][&length_mean=0.0005879062900000014,length_median=1e-08,length_sd=0.0007877836901215647,length_hpd95={1e-08,0.00183089},length_quant_5_95={1e-08,0.00182807},length_range={1e-08,0.00535402}],(DCA_1406_P_cafra_South_Africa:9.999999999999914e-09[&support=100.0][&length_mean=9.999999999999914e-09,length_median=1e-08,length_sd=(3.576351545337036e-32+5.840625309806928e-16j),length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,1e-08}],DCA_1405_P_cafra_South_Africa:1.0019999999999914e-08[&support=100.0][&length_mean=1.0019999999999914e-08,length_median=1e-08,length_sd=4.469897088295008e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}])74:0.0011359792672998674[&support=73.7][&length_mean=0.0011359792672998674,length_median=0.00089329,length_sd=0.0008433628733101678,length_hpd95={1e-08,0.00270059},length_quant_5_95={1e-08,0.00269352},length_range={1e-08,0.00550765}])94:0.006658871304347821[&support=94.3][&length_mean=0.006658871304347821,length_median=0.00627611,length_sd=0.0030273116861865763,length_hpd95={0.00111831,0.01248555},length_quant_5_95={0.00239909,0.01237508},length_range={0.00039505,0.02104386}])100:0.034816601[&support=100.0][&length_mean=0.034816601,length_median=0.034536990000000004,length_sd=0.00762813878816514,length_hpd95={0.02065206,0.05002509},length_quant_5_95={0.02274589,0.04743667},length_range={0.0119017,0.06548844}],((DCA_1397_P_maritima_Russia:0.002522820049999998[&support=100.0][&length_mean=0.002522820049999998,length_median=0.00251536,length_sd=0.0015190500257785272,length_hpd95={1e-08,0.00532473},length_quant_5_95={0.00058117,0.00532051},length_range={1e-08,0.00996678}],DCA_1399_P_subulata_Spain:0.00499295401000001[&support=100.0][&length_mean=0.00499295401000001,length_median=0.00490813,length_sd=0.002088930040570848,length_hpd95={0.00153051,0.00928674},length_quant_5_95={0.00164392,0.00867335},length_range={1e-08,0.01253197}])100:0.01457248533[&support=100.0][&length_mean=0.01457248533,length_median=0.01432754,length_sd=0.003909108640613259,length_hpd95={0.00764523,0.02295994},length_quant_5_95={0.00829742,0.0216927},length_range={0.00423569,0.02917266}],((DCA_1425_P_serraria_Italy:0.001848561439999999[&support=100.0][&length_mean=0.001848561439999999,length_median=0.001776975,length_sd=0.0013034853365077102,length_hpd95={1e-08,0.00442017},length_quant_5_95={1e-08,0.00441625},length_range={1e-08,0.00649093}],(DCA_1433_P_coronopus_Kuwait:9.50587899999993e-05[&support=100.0][&length_mean=9.50587899999993e-05,length_median=1e-08,length_sd=0.00032444634242035606,length_hpd95={1e-08,0.00084339},length_quant_5_95={1e-08,0.00084107},length_range={1e-08,0.00251922}],(DCA_1431_P_coronopus_Iran:9.999999999999914e-09[&support=100.0][&length_mean=9.999999999999914e-09,length_median=1e-08,length_sd=(3.576351545337036e-32+5.840625309806928e-16j),length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,1e-08}],DCA_1422_P_crypsoides_Saudi_Arabia:1.0009999999999914e-08[&support=100.0][&length_mean=1.0009999999999914e-08,length_median=1e-08,length_sd=3.162277660163184e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}])93:0.0014345847419354842[&support=93.0][&length_mean=0.0014345847419354842,length_median=0.001641905,length_sd=0.0010908558877034795,length_hpd95={1e-08,0.00340794},length_quant_5_95={1e-08,0.00340794},length_range={1e-08,0.00591514}])78:0.0020469996786632405[&support=77.8][&length_mean=0.0020469996786632405,length_median=0.0017134350000000001,length_sd=0.0010887290689300744,length_hpd95={0.00081584,0.00427353},length_quant_5_95={0.000829,0.00416815},length_range={1e-08,0.00764703}],(DCA_1402_P_crassifolia_Greece:0.000291098259999997[&support=100.0][&length_mean=0.000291098259999997,length_median=1e-08,length_sd=0.0007301369442580917,length_hpd95={1e-08,0.00187761},length_quant_5_95={1e-08,0.00187328},length_range={1e-08,0.00657839}],DCA_1403_P_crassifolia_Spain:0.0006683553100000043[&support=100.0][&length_mean=0.0006683553100000043,length_median=1e-08,length_sd=0.0008508522855461509,length_hpd95={1e-08,0.00245173},length_quant_5_95={1e-08,0.00243015},length_range={1e-08,0.00445658}])71:0.003449563620933518[&support=70.7][&length_mean=0.003449563620933518,length_median=0.0034102,length_sd=0.0017163115139957642,length_hpd95={1e-08,0.00636178},length_quant_5_95={0.00085272,0.0063416},length_range={1e-08,0.01097121}])100:0.009835301939999985[&support=100.0][&length_mean=0.009835301939999985,length_median=0.00968785,length_sd=0.002983809202010509,length_hpd95={0.00447332,0.0158553},length_quant_5_95={0.00511473,0.01515543},length_range={0.00106621,0.01979902}],((DCA_1424_P_coronopus_Italy:0.0010023949700000074[&support=100.0][&length_mean=0.0010023949700000074,length_median=0.00096336,length_sd=0.0009853396793865297,length_hpd95={1e-08,0.00292788},length_quant_5_95={1e-08,0.00292755},length_range={1e-08,0.00510569}],DCA_1391_P_coronopus_Algeria:1.0049999999999915e-08[&support=100.0][&length_mean=1.0049999999999915e-08,length_median=1e-08,length_sd=7.056897321044501e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}],(DCA_1390_P_coronopus_Algeria:1.0029999999999913e-08[&support=100.0][&length_mean=1.0029999999999913e-08,length_median=1e-08,length_sd=5.471740119916513e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}],DCA_1395_P_coronopus_Tunisia:0.0008603716800000074[&support=100.0][&length_mean=0.0008603716800000074,length_median=0.0008319250000000001,length_sd=0.0008406869926789732,length_hpd95={1e-08,0.00250949},length_quant_5_95={1e-08,0.00250882},length_range={1e-08,0.00428461}],(DCA_1432_P_coronopus_Spain:1.0009999999999914e-08[&support=100.0][&length_mean=1.0009999999999914e-08,length_median=1e-08,length_sd=3.162277660162784e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}],DCA_1438_P_coronopus_Montenegro:1.0039999999999913e-08[&support=100.0][&length_mean=1.0039999999999913e-08,length_median=1e-08,length_sd=6.31505185092319e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}],DCA_1392_P_coronpus_Morocco:1.0049999999999915e-08[&support=100.0][&length_mean=1.0049999999999915e-08,length_median=1e-08,length_sd=7.056897321044501e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}],DCA_1394_P_coronopus_Spain:1.0009999999999914e-08[&support=100.0][&length_mean=1.0009999999999914e-08,length_median=1e-08,length_sd=3.162277660163184e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}],DCA_1407_P_coronopus_Spain:1.0059999999999914e-08[&support=100.0][&length_mean=1.0059999999999914e-08,length_median=1e-08,length_sd=8.928590018568252e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,3e-08}])63:0.0012666598407643315[&support=62.8][&length_mean=0.0012666598407643315,length_median=0.000847645,length_sd=0.000669544155895213,length_hpd95={0.00080357,0.00258303},length_quant_5_95={0.00081316,0.00252737},length_range={1e-08,0.00424443}])63:0.001286190630914825[&support=63.4][&length_mean=0.001286190630914825,length_median=0.0008509,length_sd=0.0006798501767461136,length_hpd95={0.00079735,0.00258201},length_quant_5_95={0.00081174,0.00253633},length_range={1e-08,0.00504091}],(DCA_1033_P_coronopus_South_Africa:1.0199999999999914e-08[&support=100.0][&length_mean=1.0199999999999914e-08,length_median=1e-08,length_sd=1.470429244187491e-09,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,3e-08}],(DCA_1097_P_coronopus_Turkey:1.0009999999999914e-08[&support=100.0][&length_mean=1.0009999999999914e-08,length_median=1e-08,length_sd=3.162277660163184e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}],DCA_1036_P_coronopus_South_Africa:1.0009999999999914e-08[&support=100.0][&length_mean=1.0009999999999914e-08,length_median=1e-08,length_sd=3.1622776601625846e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}],1471:1.0089999999999914e-08[&support=100.0][&length_mean=1.0089999999999914e-08,length_median=1e-08,length_sd=9.448771310558764e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}])63:0.0005237497933227337[&support=62.9][&length_mean=0.0005237497933227337,length_median=1.2e-07,length_sd=0.0007699856204154815,length_hpd95={1e-08,0.00171561},length_quant_5_95={1e-08,0.00171214},length_range={1e-08,0.00587865}])61:0.0008325646204620443[&support=60.6][&length_mean=0.0008325646204620443,length_median=0.000829385,length_sd=0.0007884575933113642,length_hpd95={1e-08,0.00247189},length_quant_5_95={1e-08,0.00246046},length_range={1e-08,0.00419699}])100:0.009313226369999993[&support=100.0][&length_mean=0.009313226369999993,length_median=0.009163745000000001,length_sd=0.0032469418977474425,length_hpd95={0.0033547,0.0156017},length_quant_5_95={0.00420526,0.01480158},length_range={0.00082877,0.02152952}],(1473:0.0017263054800000016[&support=100.0][&length_mean=0.0017263054800000016,length_median=0.001652335,length_sd=0.0011845748256205948,length_hpd95={1e-08,0.00414056},length_quant_5_95={1e-08,0.00413787},length_range={1e-08,0.00582515}],(DCA_1024_P_crassifolia_South_Africa:1.0009999999999914e-08[&support=100.0][&length_mean=1.0009999999999914e-08,length_median=1e-08,length_sd=3.162277660162784e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}],1470:1.0009999999999914e-08[&support=100.0][&length_mean=1.0009999999999914e-08,length_median=1e-08,length_sd=3.1622776601625846e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}])88:0.0019184825854214123[&support=87.8][&length_mean=0.0019184825854214123,length_median=0.001665635,length_sd=0.0011675765907167618,length_hpd95={1e-08,0.00417347},length_quant_5_95={0.00080901,0.00417007},length_range={1e-08,0.00671149}],(DCA_1025_P_crassifolia_South_Africa:1.0049999999999915e-08[&support=100.0][&length_mean=1.0049999999999915e-08,length_median=1e-08,length_sd=7.056897321044232e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}],DCA_1026_P_crassifolia_South_Africa:1.0039999999999913e-08[&support=100.0][&length_mean=1.0039999999999913e-08,length_median=1e-08,length_sd=6.315051850922889e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}],DCA_1027_P_crassifolia_South_Africa:1.0049999999999915e-08[&support=100.0][&length_mean=1.0049999999999915e-08,length_median=1e-08,length_sd=7.056897321044321e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}],DCA_1029_P_crassifolia_South_Africa:1.0039999999999913e-08[&support=100.0][&length_mean=1.0039999999999913e-08,length_median=1e-08,length_sd=6.31505185092269e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}],DCA_1038_P_crassifolia_South_Africa:9.999999999999914e-09[&support=100.0][&length_mean=9.999999999999914e-09,length_median=1e-08,length_sd=(3.576351545337036e-32+5.840625309806928e-16j),length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,1e-08}],DCA_1396_P_crassifolia_South_Africa:1.0039999999999913e-08[&support=100.0][&length_mean=1.0039999999999913e-08,length_median=1e-08,length_sd=6.31505185092269e-10,length_hpd95={1e-08,1e-08},length_quant_5_95={1e-08,1e-08},length_range={1e-08,2e-08}])66:0.0012801575190258764[&support=65.7][&length_mean=0.0012801575190258764,length_median=0.00084,length_sd=0.0007038869793866632,length_hpd95={1e-08,0.00250921},length_quant_5_95={0.00080134,0.00250732},length_range={1e-08,0.0050049}])93:0.0019471665952890778[&support=93.4][&length_mean=0.0019471665952890778,length_median=0.00168957,length_sd=0.0013449094573581095,length_hpd95={1e-08,0.00437774},length_quant_5_95={1e-08,0.00436734},length_range={1e-08,0.00851536}])53:0.002273829359698683[&support=53.1][&length_mean=0.002273829359698683,length_median=0.00213928,length_sd=0.0013286841783812738,length_hpd95={1e-08,0.00460247},length_quant_5_95={0.0001444,0.00457568},length_range={1e-08,0.00682592}])98:0.010970966210418785[&support=97.89999999999999][&length_mean=0.010970966210418785,length_median=0.01065081,length_sd=0.003494335561691531,length_hpd95={0.0045126,0.01774134},length_quant_5_95={0.00593697,0.01706229},length_range={0.00076575,0.02361806}])100:0.016592767158634527[&support=99.6][&length_mean=0.016592767158634527,length_median=0.016447234999999998,length_sd=0.004673311998995255,length_hpd95={0.00781868,0.02547656},length_quant_5_95={0.00907241,0.02439079},length_range={0.00340013,0.0338242}])100:0.023938472362362368[&support=99.9][&length_mean=0.023938472362362368,length_median=0.02357028,length_sd=0.005624159350793365,length_hpd95={0.01385026,0.03594533},length_quant_5_95={0.01544557,0.03397366},length_range={0.00835506,0.04643044}])77:0.0012088583812010477[&support=76.6][&length_mean=0.0012088583812010477,length_median=0.000931805,length_sd=0.0011186942027297528,length_hpd95={1e-08,0.00346571},length_quant_5_95={1e-08,0.00338617},length_range={1e-08,0.00620335}],Plantago_major:0.0025460533[&support=100.0][&length_mean=0.0025460533,length_median=0.0025174250000000002,length_sd=0.0015207567569546822,length_hpd95={1e-08,0.00520409},length_quant_5_95={1e-08,0.00518186},length_range={1e-08,0.00860922}])100:0.0[&support=100.0][&length_mean=0.0,length_median=0.0,length_sd=0.0,length_hpd95={0,0},length_quant_5_95={0,0},length_range={0,0}];
END;