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program complains about subscript with nexus file #61

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cbud opened this issue Dec 8, 2015 · 3 comments
Open

program complains about subscript with nexus file #61

cbud opened this issue Dec 8, 2015 · 3 comments

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@cbud
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cbud commented Dec 8, 2015

No description provided.

@MichelleKendall
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Sorry, I'm not quite sure what you mean. Is this within the Shiny ui? Please can you provide a minimal example which replicates the error / warning?

@cbud
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cbud commented Dec 9, 2015

Loading nexus file UBUNTU OS 15 - first tree of hundreds included

During installation got this message. Yes I think it is shiny ui

Note: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.

#NEXUS

begin TREES;

TRANSLATE
    1 I4020_6_Poales_Cyperaceae_Chorizandra_multiarticulata_seq1,
    2 I4022_8_Poales_Cyperaceae_Chorizandra_sphaerocephala_seq1,
    3 I4021_7_Poales_Cyperaceae_Exocarya_sclerioides_seq1,
    4 I4024_10_Poales_Cyperaceae_Scirpodendron_ghaeri_seq1,
    5 I9902_62_Poales_Cyperaceae_Carex_lurida_seq1,
    6 I4012_3_Poales_Cyperaceae_Carex_lupulina_seq1,
    7 I4014_5_Poales_Cyperaceae_Carex_tribuloides_seq1,
    8 I4011_2_Poales_Cyperaceae_Carex_waponahkikensis_seq1,
    9 I4010_1_Poales_Cyperaceae_Carex_scoparia_seq1,
    10 I4013_4_Poales_Cyperaceae_Carex_annectens_seq1,
    11 I9717_50_Poales_Cyperaceae_Rynchospora_plumosa_seq1,
    12 I4060_20_Poales_Cyperaceae_Rhynchospora_marliniana_seq1,
    13 I9710_43_Poales_Cyperaceae_Rynchospora_intermedia_seq1,
    14 I11911_102_Poales_Cyperaceae_Rhynchospora_galeana_seq1,
    15 I9713_46_Poales_Cyperaceae_Rynchospora_megaplumosa_seq1,
    16 I4061_21_Poales_Cyperaceae_Rhynchospora_megalocarpa_seq1,
    17 I11926_117_Poales_Cyperaceae_Rhynchospora_odorata_seq1,
    18 I11891_82_Poales_Cyperaceae_Rhynchospora_brachychaeta_seq1,
    19 I9708_41_Poales_Cyperaceae_Rynchospora_globosa_seq1,
    20 I9707_40_Poales_Cyperaceae_Rynchospora_filifolia_seq1,
    21 I11916_107_Poales_Cyperaceae_Rhynchospora_harperi_seq1,
    22 I9697_30_Poales_Cyperaceae_Rynchospora_chalarocephala_seq1,
    23 I9726_59_Poales_Cyperaceae_Rynchospora_wrightiana_seq1,
    24 I11910_101_Poales_Cyperaceae_Rhynchospora_fernaldii_seq1,
    25 I9706_39_Poales_Cyperaceae_Rynchospora_fascicularis_seq1,
    26 I9698_31_Poales_Cyperaceae_Rynchospora_chapmanii_seq1,
    27 I9693_26_Poales_Cyperaceae_Rynchospora_baldwinii_seq1,
    28 I9702_35_Poales_Cyperaceae_Rynchospora_debilis_seq1,
    29 I11904_95_Poales_Cyperaceae_Rhynchospora_distans_seq1,
    30 I11909_100_Poales_Cyperaceae_Rhynchospora_fascicularis_seq1,
    31 I11895_86_Poales_Cyperaceae_Rhynchospora_capitellata_seq1,
    32 I9694_27_Poales_Cyperaceae_Rynchospora_capitellata_seq1,
    33 I9712_45_Poales_Cyperaceae_Rynchospora_leptocarpa_seq1,
    34 I9715_48_Poales_Cyperaceae_Rynchospora_microcephala_seq1,
    35 I9695_28_Poales_Cyperaceae_Rynchospora_cephalantha_seq1,
    36 I9905_64_Poales_Cyperaceae_Rhynchospora_shaferi_seq1,
    37 I11884_75_Poales_Cyperaceae_Rhynchospora_alba_seq1,
    38 I11885_76_Poales_Cyperaceae_Rhynchospora_alba_seq1,
    39 I9711_44_Poales_Cyperaceae_Rynchospora_knieskernii_seq1,
    40 I11928_119_Poales_Cyperaceae_Rhynchospora_pallida_seq1,
    41 I11921_112_Poales_Cyperaceae_Rhynchospora_macra_seq1,
    42 I4056_17_Poales_Cyperaceae_Rhynchospora_inexpansa_seq1,
    43 I11935_126_Poales_Cyperaceae_Rhynchospora_rariflora_seq1,
    44 I11945_136_Poales_Cyperaceae_Rhynchospora_stenophylla_seq1,
    45 I9724_57_Poales_Cyperaceae_Rynchospora_sulcata_seq1,
    46 I11929_120_Poales_Cyperaceae_Rhynchospora_perplexa_seq1,
    47 I9714_47_Poales_Cyperaceae_Rynchospora_microcarpa_seq1,
    48 I11903_94_Poales_Cyperaceae_Rhynchospora_decurrens_seq1,
    49 I9703_36_Poales_Cyperaceae_Rynchospora_elliotii_seq1,
    50 I9716_49_Poales_Cyperaceae_Rynchospora_miliacea_seq1,
    51 I9904_63_Poales_Cyperaceae_Rhynchospora_caduca_seq1,
    52 I11924_115_Poales_Cyperaceae_Rhynchospora_mixta_seq1,
    53 I4057_18_Poales_Cyperaceae_Rhynchospora_fusca_seq1,
    54 I11902_93_Poales_Cyperaceae_Rhynchospora_crinipes_seq1,
    55 I9709_42_Poales_Cyperaceae_Rynchospora_globularis_saxicola_seq1,
    56 I11917_108_Poales_Cyperaceae_Rhynchospora_harveyi_seq1,
    57 I11915_106_Poales_Cyperaceae_Rhynchospora_grayi_seq1,
    58 I4054_15_Poales_Cyperaceae_Rhynchospora_globularis_globularis_seq1,
    59 I11914_105_Poales_Cyperaceae_Rhynchospora_globularis_pinetorum_seq1,
    60 I11932_123_Poales_Cyperaceae_Rhynchospora_punctata_seq1,
    61 I11936_127_Poales_Cyperaceae_Rhynchospora_recognita_seq1,
    62 I9700_33_Poales_Cyperaceae_Rynchospora_compressa_seq1,
    63 I9699_32_Poales_Cyperaceae_Rynchospora_colorata_seq1,
    64 I11893_84_Poales_Cyperaceae_Rhynchospora_bucherorum_seq1,
    65 I9718_51_Poales_Cyperaceae_Rynchospora_pruinosa_seq1,
    66 I9701_34_Poales_Cyperaceae_Rynchospora_cubensis_seq1,
    67 I9719_52_Poales_Cyperaceae_Rynchospora_pusilla_seq1,
    68 I11906_97_Poales_Cyperaceae_Rhynchospora_divergens_seq1,
    69 I11888_79_Poales_Cyperaceae_Rhynchospora_barrosiana_seq1,
    70 I11940_131_Poales_Cyperaceae_Rhynchospora_rugosa_bruhl_seq1,
    71 I11942_133_Poales_Cyperaceae_Rhynchospora_rugosa_copeland_seq1,
    72 I9721_54_Poales_Cyperaceae_Rynchospora_rugosa_brownii_seq1,
    73 I9727_60_Poales_Cyperaceae_Rynchospora_chinensis_spiciformis_seq1,
    74 I9728_61_Poales_Cyperaceae_Rynchospora_rugosalavarum_seq1,
    75 I11894_85_Poales_Cyperaceae_Rhynchospora_californica_seq1,
    76 I11892_83_Poales_Cyperaceae_Rhynchospora_brasiliensis_seq1,
    77 I11923_114_Poales_Cyperaceae_Rhynchospora_marisculus_seq1,
    78 I11941_132_Poales_Cyperaceae_Rhynchospora_rugosa_wilson_seq1,
    79 I11947_138_Poales_Cyperaceae_Rhynchospora_vulcani_seq1,
    80 I11943_134_Poales_Cyperaceae_Rhynchospora_schiedeana_seq1,
    81 I11933_124_Poales_Cyperaceae_Rhynchospora_racemosa_seq1,
    82 I11890_81_Poales_Cyperaceae_Rhynchospora_biflora_seq1,
    83 I11930_121_Poales_Cyperaceae_Rhynchospora_polyphylla_seq1,
    84 I11897_88_Poales_Cyperaceae_Rhynchospora_comata_seq1,
    85 I11919_110_Poales_Cyperaceae_Rhynchospora_imeriensis_seq1,
    86 I9696_29_Poales_Cyperaceae_Rynchospora_cephalotes_seq1,
    87 I11878_69_Poales_Cyperaceae_Pleurostachys_stricta_seq1,
    88 I9690_23_Poales_Cyperaceae_Pleurostachys_sp2_seq1,
    89 I9689_22_Poales_Cyperaceae_Pleurostachys_sp1_seq1,
    90 I11881_72_Poales_Cyperaceae_Pleurostachys_urvillei_seq1,
    91 I11880_71_Poales_Cyperaceae_Pleurostachys_tenuiflora_seq1,
    92 I11879_70_Poales_Cyperaceae_Pleurostachys_tenuiflora_seq1,
    93 I11874_65_Poales_Cyperaceae_Pleurostachys_angustifolia_seq1,
    94 I11876_67_Poales_Cyperaceae_Pleurostachys_gaudichaudii_seq1,
    95 I11877_68_Poales_Cyperaceae_Pleurostachys_graminifolia_seq1,
    96 I11912_103_Poales_Cyperaceae_Rhynchospora_gigantea_seq1,
    97 I11900_91_Poales_Cyperaceae_Rhynchospora_corymbosa_seq1,
    98 I11901_92_Poales_Cyperaceae_Rhynchospora_corymbosa_seq1,
    99 I11899_90_Poales_Cyperaceae_Rhynchospora_corymbosa_seq1,
    100 I4051_12_Poales_Cyperaceae_Rhynchospora_inundata_seq1,
    101 I4050_11_Poales_Cyperaceae_Rhynchospora_careyana_seq1,
    102 I4052_13_Poales_Cyperaceae_Rhynchospora_corniculata_seq1,
    103 I11922_113_Poales_Cyperaceae_Rhynchospora_macrostachya_seq1,
    104 I11887_78_Poales_Cyperaceae_Rhynchospora_barbata_seq1,
    105 I11920_111_Poales_Cyperaceae_Rhynchospora_longisetis_seq1,
    106 I11883_74_Poales_Cyperaceae_Rhynchospora_affinis_seq1,
    107 I9720_53_Poales_Cyperaceae_Rynchospora_rubra_seq1,
    108 I11898_89_Poales_Cyperaceae_Rhynchospora_consanguinea_seq1,
    109 I11944_135_Poales_Cyperaceae_Rhynchospora_speciosa_seq1,
    110 I11886_77_Poales_Cyperaceae_Rhynchospora_albiceps_seq1,
    111 I11918_109_Poales_Cyperaceae_Rhynchospora_holoschoenoides_seq1,
    112 I4053_14_Poales_Cyperaceae_Rhynchospora_tracyi_seq1,
    113 I11889_80_Poales_Cyperaceae_Rhynchospora_berteroi_seq1,
    114 I9723_56_Poales_Cyperaceae_Rynchospora_seslerioides_seq1,
    115 I11925_116_Poales_Cyperaceae_Rhynchospora_nivea_seq1,
    116 I4055_16_Poales_Cyperaceae_Rhynchospora_latifolia_seq1,
    117 I11934_125_Poales_Cyperaceae_Rhynchospora_radicans_seq1,
    118 I11931_122_Poales_Cyperaceae_Rhynchospora_pubera_seq1,
    119 I11896_87_Poales_Cyperaceae_Rhynchospora_ciliolata_seq1,
    120 I11939_130_Poales_Cyperaceae_Rhynchospora_robusta_seq1,
    121 I11908_99_Poales_Cyperaceae_Rhynchospora_eximia_seq1,
    122 I4058_19_Poales_Cyperaceae_Rhynchospora_nitens_seq1,
    123 I9722_55_Poales_Cyperaceae_Rynchospora_scirpoides_seq1,
    124 I11905_96_Poales_Cyperaceae_Rhynchospora_divaricata_seq1,
    125 I9725_58_Poales_Cyperaceae_Rynchospora_tenerrima_seq1,
    126 I11882_73_Poales_Cyperaceae_Rhynchospora_sp_Thomas_seq1,
    127 I9704_37_Poales_Cyperaceae_Rynchospora_emaciata_seq1,
    128 I11946_137_Poales_Cyperaceae_Rhynchospora_tenuis_seq1,
    129 I11938_129_Poales_Cyperaceae_Rhynchospora_riparia_seq1,
    130 I9692_25_Poales_Cyperaceae_Rynchospora_abberans_seq1,
    131 I9691_24_Poales_Cyperaceae_Rynchospora_sp2_Wilson_seq1,
    132 I11937_128_Poales_Cyperaceae_Rhynchospora_riedeliana_seq1,
    133 I11907_98_Poales_Cyperaceae_Rhynchospora_elatior_seq1,
    134 I11913_104_Poales_Cyperaceae_Rhynchospora_glaziovii_seq1,
    135 I9705_38_Poales_Cyperaceae_Rynchospora_exaltata_seq1,
    136 I4023_9_Poales_Cyperaceae_Hypolytrum_nemorum_seq1;


TREE tree_1 = ((((1:0.027294,2:0.031465):0.035132,3:0.032433):0.029883,(4:0.066078,(((5:0.00659,6:0.005689):0.022575,(((7:0.001937,8:0.000001):0.000001,9:0.00252):0.017216,10:0.014062):0.022292):0.081495,((((11:0.002102,12:0.004944):0.00432,(13:0.003012,(14:0.00783,15:0.005824):0.000805):0.00858):0.00704,((16:0.000001,17:0.000001):0.01382,(((((18:0.003691,((19:0.000001,20:0.000001):0.003212,21:0.007451):0.000939):0.003433,((22:0.000001,(23:0.000001,24:0.000001):0.000001):0.009099,((25:0.000972,26:0.003866):0.000478,((27:0.003711,28:0.002171):0.00282,29:0.002886):0.000001):0.003994):0.000465):0.002318,30:0.001986):0.000702,(((31:0.00144,32:0.002891):0.000964,(33:0.002769,((34:0.002553,35:0.001021):0.000492,36:0.002597):0.000002):0.003871):0.006287,((((37:0.000973,38:0.000489):0.002279,39:0.005015):0.001922,(40:0.000001,41:0.000001):0.007105):0.002093,42:0.006841):0.000001):0.000964):0.000499,(((43:0.002424,44:0.002436):0.004367,(((45:0.001723,(46:0.001173,47:0.002208):0.000481):0.002396,(48:0.002941,49:0.004276):0.003268):0.003142,(((50:0.003099,(51:0.00812,52:0.003878):0.001989):0.000993,((53:0.000001,54:0.000001):0.005323,((((55:0.004644,(56:0.003093,57:0.00065):0.001013):0.001287,(58:0.000001,59:0.000001):0.003482):0.001444,60:0.00447):0.000892,(61:0.001447,62:0.001933):0.000001):0.004343):0.000001):0.000496,63:0.000001):0.000001):0.000001):0.001994,((64:0.004424,(65:0.005366,66:0.001469):0.000001):0.003375,((67:0.00288,68:0.007836):0.006363,(69:0.00097,((((70:0.000962,(71:0.000001,72:0.000001):0.000961):0.000481,(73:0.000001,(74:0.000001,75:0.001673):0.000001):0.001796):0.000001,(76:0.002889,77:0.001445):0.000001):0.000514,78:0.003369):0.000505):0.005587):0.000001):0.001014):0.002384):0.003864):0.003769):0.039697,((((79:0.004867,80:0.00325):0.008655,((81:0.002892,82:0.000776):0.005173,83:0.007049):0.005466):0.046206,(84:0.008576,(85:0.009187,86:0.006891):0.000814):0.058813):0.020895,((87:0.004492,(88:0.011162,(89:0.010587,((90:0.007754,((91:0.001779,92:0.000001):0.00283,(93:0.00113,94:0.013844):0.00136):0.005718):0.001823,95:0.006448):0.00099):0.003212):0.002098):0.028662,((((96:0.005311,((97:0.001132,98:0.001135):0.006428,99:0.000001):0.001166):0.001074,(100:0.005169,(101:0.000001,(102:0.00448,103:0.000582):0.000001):0.003161):0.003339):0.039844,(((104:0.05836,((105:0.004525,106:0.00655):0.006397,107:0.003715):0.022655):0.012829,(108:0.000707,(109:0.002601,110:0.003531):0.007472):0.018917):0.01585,(111:0.022189,112:0.023298):0.031873):0.005787):0.09393,(((113:0.033172,(((114:0.012414,(115:0.005637,116:0.005037):0.00885):0.012933,(117:0.017625,118:0.011354):0.002148):0.00025,119:0.026112):0.012042):0.034505,((120:0.012176,(121:0.024877,((122:0.000536,123:0.000559):0.010636,124:0.016276):0.003218):0.011975):0.018538,(125:0.039123,(((126:0.013476,127:0.002148):0.017191,128:0.028731):0.011179,129:0.032877):0.007292):0.007439):0.007158):0.065056,(((130:0.000001,131:0.000001):0.02613,(132:0.000001,133:0.000001):0.010596):0.033234,(134:0.001864,135:0.000544):0.038453):0.019372):0.002816):0.007243):0.003907):0.008444):0.057195):0.091229):0.010136):0.45,136:0.45);

end;

@MichelleKendall
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I am unable to replicate your problem. Since there is only one tree here treescape of course cannot make an MDS (it needs at least three trees) so I simply adapted your example to include 10 random trees. I don't get any error messages with the nexus file content below. What is the error message you get, and why do you think it relates to subscripts?

#NEXUS
[R-package APE, Wed Dec 09 16:19:57 2015]

BEGIN TAXA;
    DIMENSIONS NTAX = 136;
    TAXLABELS
        I4020_6_Poales_Cyperaceae_Chorizandra_multiarticulata_seq1
        I4022_8_Poales_Cyperaceae_Chorizandra_sphaerocephala_seq1
        I4021_7_Poales_Cyperaceae_Exocarya_sclerioides_seq1
        I4024_10_Poales_Cyperaceae_Scirpodendron_ghaeri_seq1
        I9902_62_Poales_Cyperaceae_Carex_lurida_seq1
        I4012_3_Poales_Cyperaceae_Carex_lupulina_seq1
        I4014_5_Poales_Cyperaceae_Carex_tribuloides_seq1
        I4011_2_Poales_Cyperaceae_Carex_waponahkikensis_seq1
        I4010_1_Poales_Cyperaceae_Carex_scoparia_seq1
        I4013_4_Poales_Cyperaceae_Carex_annectens_seq1
        I9717_50_Poales_Cyperaceae_Rynchospora_plumosa_seq1
        I4060_20_Poales_Cyperaceae_Rhynchospora_marliniana_seq1
        I9710_43_Poales_Cyperaceae_Rynchospora_intermedia_seq1
        I11911_102_Poales_Cyperaceae_Rhynchospora_galeana_seq1
        I9713_46_Poales_Cyperaceae_Rynchospora_megaplumosa_seq1
        I4061_21_Poales_Cyperaceae_Rhynchospora_megalocarpa_seq1
        I11926_117_Poales_Cyperaceae_Rhynchospora_odorata_seq1
        I11891_82_Poales_Cyperaceae_Rhynchospora_brachychaeta_seq1
        I9708_41_Poales_Cyperaceae_Rynchospora_globosa_seq1
        I9707_40_Poales_Cyperaceae_Rynchospora_filifolia_seq1
        I11916_107_Poales_Cyperaceae_Rhynchospora_harperi_seq1
        I9697_30_Poales_Cyperaceae_Rynchospora_chalarocephala_seq1
        I9726_59_Poales_Cyperaceae_Rynchospora_wrightiana_seq1
        I11910_101_Poales_Cyperaceae_Rhynchospora_fernaldii_seq1
        I9706_39_Poales_Cyperaceae_Rynchospora_fascicularis_seq1
        I9698_31_Poales_Cyperaceae_Rynchospora_chapmanii_seq1
        I9693_26_Poales_Cyperaceae_Rynchospora_baldwinii_seq1
        I9702_35_Poales_Cyperaceae_Rynchospora_debilis_seq1
        I11904_95_Poales_Cyperaceae_Rhynchospora_distans_seq1
        I11909_100_Poales_Cyperaceae_Rhynchospora_fascicularis_seq1
        I11895_86_Poales_Cyperaceae_Rhynchospora_capitellata_seq1
        I9694_27_Poales_Cyperaceae_Rynchospora_capitellata_seq1
        I9712_45_Poales_Cyperaceae_Rynchospora_leptocarpa_seq1
        I9715_48_Poales_Cyperaceae_Rynchospora_microcephala_seq1
        I9695_28_Poales_Cyperaceae_Rynchospora_cephalantha_seq1
        I9905_64_Poales_Cyperaceae_Rhynchospora_shaferi_seq1
        I11884_75_Poales_Cyperaceae_Rhynchospora_alba_seq1
        I11885_76_Poales_Cyperaceae_Rhynchospora_alba_seq1
        I9711_44_Poales_Cyperaceae_Rynchospora_knieskernii_seq1
        I11928_119_Poales_Cyperaceae_Rhynchospora_pallida_seq1
        I11921_112_Poales_Cyperaceae_Rhynchospora_macra_seq1
        I4056_17_Poales_Cyperaceae_Rhynchospora_inexpansa_seq1
        I11935_126_Poales_Cyperaceae_Rhynchospora_rariflora_seq1
        I11945_136_Poales_Cyperaceae_Rhynchospora_stenophylla_seq1
        I9724_57_Poales_Cyperaceae_Rynchospora_sulcata_seq1
        I11929_120_Poales_Cyperaceae_Rhynchospora_perplexa_seq1
        I9714_47_Poales_Cyperaceae_Rynchospora_microcarpa_seq1
        I11903_94_Poales_Cyperaceae_Rhynchospora_decurrens_seq1
        I9703_36_Poales_Cyperaceae_Rynchospora_elliotii_seq1
        I9716_49_Poales_Cyperaceae_Rynchospora_miliacea_seq1
        I9904_63_Poales_Cyperaceae_Rhynchospora_caduca_seq1
        I11924_115_Poales_Cyperaceae_Rhynchospora_mixta_seq1
        I4057_18_Poales_Cyperaceae_Rhynchospora_fusca_seq1
        I11902_93_Poales_Cyperaceae_Rhynchospora_crinipes_seq1
        I9709_42_Poales_Cyperaceae_Rynchospora_globularis_saxicola_seq1
        I11917_108_Poales_Cyperaceae_Rhynchospora_harveyi_seq1
        I11915_106_Poales_Cyperaceae_Rhynchospora_grayi_seq1
        I4054_15_Poales_Cyperaceae_Rhynchospora_globularis_globularis_seq1
        I11914_105_Poales_Cyperaceae_Rhynchospora_globularis_pinetorum_seq1
        I11932_123_Poales_Cyperaceae_Rhynchospora_punctata_seq1
        I11936_127_Poales_Cyperaceae_Rhynchospora_recognita_seq1
        I9700_33_Poales_Cyperaceae_Rynchospora_compressa_seq1
        I9699_32_Poales_Cyperaceae_Rynchospora_colorata_seq1
        I11893_84_Poales_Cyperaceae_Rhynchospora_bucherorum_seq1
        I9718_51_Poales_Cyperaceae_Rynchospora_pruinosa_seq1
        I9701_34_Poales_Cyperaceae_Rynchospora_cubensis_seq1
        I9719_52_Poales_Cyperaceae_Rynchospora_pusilla_seq1
        I11906_97_Poales_Cyperaceae_Rhynchospora_divergens_seq1
        I11888_79_Poales_Cyperaceae_Rhynchospora_barrosiana_seq1
        I11940_131_Poales_Cyperaceae_Rhynchospora_rugosa_bruhl_seq1
        I11942_133_Poales_Cyperaceae_Rhynchospora_rugosa_copeland_seq1
        I9721_54_Poales_Cyperaceae_Rynchospora_rugosa_brownii_seq1
        I9727_60_Poales_Cyperaceae_Rynchospora_chinensis_spiciformis_seq1
        I9728_61_Poales_Cyperaceae_Rynchospora_rugosalavarum_seq1
        I11894_85_Poales_Cyperaceae_Rhynchospora_californica_seq1
        I11892_83_Poales_Cyperaceae_Rhynchospora_brasiliensis_seq1
        I11923_114_Poales_Cyperaceae_Rhynchospora_marisculus_seq1
        I11941_132_Poales_Cyperaceae_Rhynchospora_rugosa_wilson_seq1
        I11947_138_Poales_Cyperaceae_Rhynchospora_vulcani_seq1
        I11943_134_Poales_Cyperaceae_Rhynchospora_schiedeana_seq1
        I11933_124_Poales_Cyperaceae_Rhynchospora_racemosa_seq1
        I11890_81_Poales_Cyperaceae_Rhynchospora_biflora_seq1
        I11930_121_Poales_Cyperaceae_Rhynchospora_polyphylla_seq1
        I11897_88_Poales_Cyperaceae_Rhynchospora_comata_seq1
        I11919_110_Poales_Cyperaceae_Rhynchospora_imeriensis_seq1
        I9696_29_Poales_Cyperaceae_Rynchospora_cephalotes_seq1
        I11878_69_Poales_Cyperaceae_Pleurostachys_stricta_seq1
        I9690_23_Poales_Cyperaceae_Pleurostachys_sp2_seq1
        I9689_22_Poales_Cyperaceae_Pleurostachys_sp1_seq1
        I11881_72_Poales_Cyperaceae_Pleurostachys_urvillei_seq1
        I11880_71_Poales_Cyperaceae_Pleurostachys_tenuiflora_seq1
        I11879_70_Poales_Cyperaceae_Pleurostachys_tenuiflora_seq1
        I11874_65_Poales_Cyperaceae_Pleurostachys_angustifolia_seq1
        I11876_67_Poales_Cyperaceae_Pleurostachys_gaudichaudii_seq1
        I11877_68_Poales_Cyperaceae_Pleurostachys_graminifolia_seq1
        I11912_103_Poales_Cyperaceae_Rhynchospora_gigantea_seq1
        I11900_91_Poales_Cyperaceae_Rhynchospora_corymbosa_seq1
        I11901_92_Poales_Cyperaceae_Rhynchospora_corymbosa_seq1
        I11899_90_Poales_Cyperaceae_Rhynchospora_corymbosa_seq1
        I4051_12_Poales_Cyperaceae_Rhynchospora_inundata_seq1
        I4050_11_Poales_Cyperaceae_Rhynchospora_careyana_seq1
        I4052_13_Poales_Cyperaceae_Rhynchospora_corniculata_seq1
        I11922_113_Poales_Cyperaceae_Rhynchospora_macrostachya_seq1
        I11887_78_Poales_Cyperaceae_Rhynchospora_barbata_seq1
        I11920_111_Poales_Cyperaceae_Rhynchospora_longisetis_seq1
        I11883_74_Poales_Cyperaceae_Rhynchospora_affinis_seq1
        I9720_53_Poales_Cyperaceae_Rynchospora_rubra_seq1
        I11898_89_Poales_Cyperaceae_Rhynchospora_consanguinea_seq1
        I11944_135_Poales_Cyperaceae_Rhynchospora_speciosa_seq1
        I11886_77_Poales_Cyperaceae_Rhynchospora_albiceps_seq1
        I11918_109_Poales_Cyperaceae_Rhynchospora_holoschoenoides_seq1
        I4053_14_Poales_Cyperaceae_Rhynchospora_tracyi_seq1
        I11889_80_Poales_Cyperaceae_Rhynchospora_berteroi_seq1
        I9723_56_Poales_Cyperaceae_Rynchospora_seslerioides_seq1
        I11925_116_Poales_Cyperaceae_Rhynchospora_nivea_seq1
        I4055_16_Poales_Cyperaceae_Rhynchospora_latifolia_seq1
        I11934_125_Poales_Cyperaceae_Rhynchospora_radicans_seq1
        I11931_122_Poales_Cyperaceae_Rhynchospora_pubera_seq1
        I11896_87_Poales_Cyperaceae_Rhynchospora_ciliolata_seq1
        I11939_130_Poales_Cyperaceae_Rhynchospora_robusta_seq1
        I11908_99_Poales_Cyperaceae_Rhynchospora_eximia_seq1
        I4058_19_Poales_Cyperaceae_Rhynchospora_nitens_seq1
        I9722_55_Poales_Cyperaceae_Rynchospora_scirpoides_seq1
        I11905_96_Poales_Cyperaceae_Rhynchospora_divaricata_seq1
        I9725_58_Poales_Cyperaceae_Rynchospora_tenerrima_seq1
        I11882_73_Poales_Cyperaceae_Rhynchospora_sp_Thomas_seq1
        I9704_37_Poales_Cyperaceae_Rynchospora_emaciata_seq1
        I11946_137_Poales_Cyperaceae_Rhynchospora_tenuis_seq1
        I11938_129_Poales_Cyperaceae_Rhynchospora_riparia_seq1
        I9692_25_Poales_Cyperaceae_Rynchospora_abberans_seq1
        I9691_24_Poales_Cyperaceae_Rynchospora_sp2_Wilson_seq1
        I11937_128_Poales_Cyperaceae_Rhynchospora_riedeliana_seq1
        I11907_98_Poales_Cyperaceae_Rhynchospora_elatior_seq1
        I11913_104_Poales_Cyperaceae_Rhynchospora_glaziovii_seq1
        I970538Poales_Cyperaceae_Rynchospora_exaltata_seq1
        I4023_9_Poales_Cyperaceae_Hypolytrum_nemorum_seq1
    ;
END;
BEGIN TREES;
    TRANSLATE
        1   I4020_6_Poales_Cyperaceae_Chorizandra_multiarticulata_seq1,
        2   I4022_8_Poales_Cyperaceae_Chorizandra_sphaerocephala_seq1,
        3   I4021_7_Poales_Cyperaceae_Exocarya_sclerioides_seq1,
        4   I4024_10_Poales_Cyperaceae_Scirpodendron_ghaeri_seq1,
        5   I9902_62_Poales_Cyperaceae_Carex_lurida_seq1,
        6   I4012_3_Poales_Cyperaceae_Carex_lupulina_seq1,
        7   I4014_5_Poales_Cyperaceae_Carex_tribuloides_seq1,
        8   I4011_2_Poales_Cyperaceae_Carex_waponahkikensis_seq1,
        9   I4010_1_Poales_Cyperaceae_Carex_scoparia_seq1,
        10  I4013_4_Poales_Cyperaceae_Carex_annectens_seq1,
        11  I9717_50_Poales_Cyperaceae_Rynchospora_plumosa_seq1,
        12  I4060_20_Poales_Cyperaceae_Rhynchospora_marliniana_seq1,
        13  I9710_43_Poales_Cyperaceae_Rynchospora_intermedia_seq1,
        14  I11911_102_Poales_Cyperaceae_Rhynchospora_galeana_seq1,
        15  I9713_46_Poales_Cyperaceae_Rynchospora_megaplumosa_seq1,
        16  I4061_21_Poales_Cyperaceae_Rhynchospora_megalocarpa_seq1,
        17  I11926_117_Poales_Cyperaceae_Rhynchospora_odorata_seq1,
        18  I11891_82_Poales_Cyperaceae_Rhynchospora_brachychaeta_seq1,
        19  I9708_41_Poales_Cyperaceae_Rynchospora_globosa_seq1,
        20  I9707_40_Poales_Cyperaceae_Rynchospora_filifolia_seq1,
        21  I11916_107_Poales_Cyperaceae_Rhynchospora_harperi_seq1,
        22  I9697_30_Poales_Cyperaceae_Rynchospora_chalarocephala_seq1,
        23  I9726_59_Poales_Cyperaceae_Rynchospora_wrightiana_seq1,
        24  I11910_101_Poales_Cyperaceae_Rhynchospora_fernaldii_seq1,
        25  I9706_39_Poales_Cyperaceae_Rynchospora_fascicularis_seq1,
        26  I9698_31_Poales_Cyperaceae_Rynchospora_chapmanii_seq1,
        27  I9693_26_Poales_Cyperaceae_Rynchospora_baldwinii_seq1,
        28  I9702_35_Poales_Cyperaceae_Rynchospora_debilis_seq1,
        29  I11904_95_Poales_Cyperaceae_Rhynchospora_distans_seq1,
        30  I11909_100_Poales_Cyperaceae_Rhynchospora_fascicularis_seq1,
        31  I11895_86_Poales_Cyperaceae_Rhynchospora_capitellata_seq1,
        32  I9694_27_Poales_Cyperaceae_Rynchospora_capitellata_seq1,
        33  I9712_45_Poales_Cyperaceae_Rynchospora_leptocarpa_seq1,
        34  I9715_48_Poales_Cyperaceae_Rynchospora_microcephala_seq1,
        35  I9695_28_Poales_Cyperaceae_Rynchospora_cephalantha_seq1,
        36  I9905_64_Poales_Cyperaceae_Rhynchospora_shaferi_seq1,
        37  I11884_75_Poales_Cyperaceae_Rhynchospora_alba_seq1,
        38  I11885_76_Poales_Cyperaceae_Rhynchospora_alba_seq1,
        39  I9711_44_Poales_Cyperaceae_Rynchospora_knieskernii_seq1,
        40  I11928_119_Poales_Cyperaceae_Rhynchospora_pallida_seq1,
        41  I11921_112_Poales_Cyperaceae_Rhynchospora_macra_seq1,
        42  I4056_17_Poales_Cyperaceae_Rhynchospora_inexpansa_seq1,
        43  I11935_126_Poales_Cyperaceae_Rhynchospora_rariflora_seq1,
        44  I11945_136_Poales_Cyperaceae_Rhynchospora_stenophylla_seq1,
        45  I9724_57_Poales_Cyperaceae_Rynchospora_sulcata_seq1,
        46  I11929_120_Poales_Cyperaceae_Rhynchospora_perplexa_seq1,
        47  I9714_47_Poales_Cyperaceae_Rynchospora_microcarpa_seq1,
        48  I11903_94_Poales_Cyperaceae_Rhynchospora_decurrens_seq1,
        49  I9703_36_Poales_Cyperaceae_Rynchospora_elliotii_seq1,
        50  I9716_49_Poales_Cyperaceae_Rynchospora_miliacea_seq1,
        51  I9904_63_Poales_Cyperaceae_Rhynchospora_caduca_seq1,
        52  I11924_115_Poales_Cyperaceae_Rhynchospora_mixta_seq1,
        53  I4057_18_Poales_Cyperaceae_Rhynchospora_fusca_seq1,
        54  I11902_93_Poales_Cyperaceae_Rhynchospora_crinipes_seq1,
        55  I9709_42_Poales_Cyperaceae_Rynchospora_globularis_saxicola_seq1,
        56  I11917_108_Poales_Cyperaceae_Rhynchospora_harveyi_seq1,
        57  I11915_106_Poales_Cyperaceae_Rhynchospora_grayi_seq1,
        58  I4054_15_Poales_Cyperaceae_Rhynchospora_globularis_globularis_seq1,
        59  I11914_105_Poales_Cyperaceae_Rhynchospora_globularis_pinetorum_seq1,
        60  I11932_123_Poales_Cyperaceae_Rhynchospora_punctata_seq1,
        61  I11936_127_Poales_Cyperaceae_Rhynchospora_recognita_seq1,
        62  I9700_33_Poales_Cyperaceae_Rynchospora_compressa_seq1,
        63  I9699_32_Poales_Cyperaceae_Rynchospora_colorata_seq1,
        64  I11893_84_Poales_Cyperaceae_Rhynchospora_bucherorum_seq1,
        65  I9718_51_Poales_Cyperaceae_Rynchospora_pruinosa_seq1,
        66  I9701_34_Poales_Cyperaceae_Rynchospora_cubensis_seq1,
        67  I9719_52_Poales_Cyperaceae_Rynchospora_pusilla_seq1,
        68  I11906_97_Poales_Cyperaceae_Rhynchospora_divergens_seq1,
        69  I11888_79_Poales_Cyperaceae_Rhynchospora_barrosiana_seq1,
        70  I11940_131_Poales_Cyperaceae_Rhynchospora_rugosa_bruhl_seq1,
        71  I11942_133_Poales_Cyperaceae_Rhynchospora_rugosa_copeland_seq1,
        72  I9721_54_Poales_Cyperaceae_Rynchospora_rugosa_brownii_seq1,
        73  I9727_60_Poales_Cyperaceae_Rynchospora_chinensis_spiciformis_seq1,
        74  I9728_61_Poales_Cyperaceae_Rynchospora_rugosalavarum_seq1,
        75  I11894_85_Poales_Cyperaceae_Rhynchospora_californica_seq1,
        76  I11892_83_Poales_Cyperaceae_Rhynchospora_brasiliensis_seq1,
        77  I11923_114_Poales_Cyperaceae_Rhynchospora_marisculus_seq1,
        78  I11941_132_Poales_Cyperaceae_Rhynchospora_rugosa_wilson_seq1,
        79  I11947_138_Poales_Cyperaceae_Rhynchospora_vulcani_seq1,
        80  I11943_134_Poales_Cyperaceae_Rhynchospora_schiedeana_seq1,
        81  I11933_124_Poales_Cyperaceae_Rhynchospora_racemosa_seq1,
        82  I11890_81_Poales_Cyperaceae_Rhynchospora_biflora_seq1,
        83  I11930_121_Poales_Cyperaceae_Rhynchospora_polyphylla_seq1,
        84  I11897_88_Poales_Cyperaceae_Rhynchospora_comata_seq1,
        85  I11919_110_Poales_Cyperaceae_Rhynchospora_imeriensis_seq1,
        86  I9696_29_Poales_Cyperaceae_Rynchospora_cephalotes_seq1,
        87  I11878_69_Poales_Cyperaceae_Pleurostachys_stricta_seq1,
        88  I9690_23_Poales_Cyperaceae_Pleurostachys_sp2_seq1,
        89  I9689_22_Poales_Cyperaceae_Pleurostachys_sp1_seq1,
        90  I11881_72_Poales_Cyperaceae_Pleurostachys_urvillei_seq1,
        91  I11880_71_Poales_Cyperaceae_Pleurostachys_tenuiflora_seq1,
        92  I11879_70_Poales_Cyperaceae_Pleurostachys_tenuiflora_seq1,
        93  I11874_65_Poales_Cyperaceae_Pleurostachys_angustifolia_seq1,
        94  I11876_67_Poales_Cyperaceae_Pleurostachys_gaudichaudii_seq1,
        95  I11877_68_Poales_Cyperaceae_Pleurostachys_graminifolia_seq1,
        96  I11912_103_Poales_Cyperaceae_Rhynchospora_gigantea_seq1,
        97  I11900_91_Poales_Cyperaceae_Rhynchospora_corymbosa_seq1,
        98  I11901_92_Poales_Cyperaceae_Rhynchospora_corymbosa_seq1,
        99  I11899_90_Poales_Cyperaceae_Rhynchospora_corymbosa_seq1,
        100 I4051_12_Poales_Cyperaceae_Rhynchospora_inundata_seq1,
        101 I4050_11_Poales_Cyperaceae_Rhynchospora_careyana_seq1,
        102 I4052_13_Poales_Cyperaceae_Rhynchospora_corniculata_seq1,
        103 I11922_113_Poales_Cyperaceae_Rhynchospora_macrostachya_seq1,
        104 I11887_78_Poales_Cyperaceae_Rhynchospora_barbata_seq1,
        105 I11920_111_Poales_Cyperaceae_Rhynchospora_longisetis_seq1,
        106 I11883_74_Poales_Cyperaceae_Rhynchospora_affinis_seq1,
        107 I9720_53_Poales_Cyperaceae_Rynchospora_rubra_seq1,
        108 I11898_89_Poales_Cyperaceae_Rhynchospora_consanguinea_seq1,
        109 I11944_135_Poales_Cyperaceae_Rhynchospora_speciosa_seq1,
        110 I11886_77_Poales_Cyperaceae_Rhynchospora_albiceps_seq1,
        111 I11918_109_Poales_Cyperaceae_Rhynchospora_holoschoenoides_seq1,
        112 I4053_14_Poales_Cyperaceae_Rhynchospora_tracyi_seq1,
        113 I11889_80_Poales_Cyperaceae_Rhynchospora_berteroi_seq1,
        114 I9723_56_Poales_Cyperaceae_Rynchospora_seslerioides_seq1,
        115 I11925_116_Poales_Cyperaceae_Rhynchospora_nivea_seq1,
        116 I4055_16_Poales_Cyperaceae_Rhynchospora_latifolia_seq1,
        117 I11934_125_Poales_Cyperaceae_Rhynchospora_radicans_seq1,
        118 I11931_122_Poales_Cyperaceae_Rhynchospora_pubera_seq1,
        119 I11896_87_Poales_Cyperaceae_Rhynchospora_ciliolata_seq1,
        120 I11939_130_Poales_Cyperaceae_Rhynchospora_robusta_seq1,
        121 I11908_99_Poales_Cyperaceae_Rhynchospora_eximia_seq1,
        122 I4058_19_Poales_Cyperaceae_Rhynchospora_nitens_seq1,
        123 I9722_55_Poales_Cyperaceae_Rynchospora_scirpoides_seq1,
        124 I11905_96_Poales_Cyperaceae_Rhynchospora_divaricata_seq1,
        125 I9725_58_Poales_Cyperaceae_Rynchospora_tenerrima_seq1,
        126 I11882_73_Poales_Cyperaceae_Rhynchospora_sp_Thomas_seq1,
        127 I9704_37_Poales_Cyperaceae_Rynchospora_emaciata_seq1,
        128 I11946_137_Poales_Cyperaceae_Rhynchospora_tenuis_seq1,
        129 I11938_129_Poales_Cyperaceae_Rhynchospora_riparia_seq1,
        130 I9692_25_Poales_Cyperaceae_Rynchospora_abberans_seq1,
        131 I9691_24_Poales_Cyperaceae_Rynchospora_sp2_Wilson_seq1,
        132 I11937_128_Poales_Cyperaceae_Rhynchospora_riedeliana_seq1,
        133 I11907_98_Poales_Cyperaceae_Rhynchospora_elatior_seq1,
        134 I11913_104_Poales_Cyperaceae_Rhynchospora_glaziovii_seq1,
        135 I970538Poales_Cyperaceae_Rynchospora_exaltata_seq1,
        136 I4023_9_Poales_Cyperaceae_Hypolytrum_nemorum_seq1
    ;
    TREE_1 = [&R] ((((1:0.027294,2:0.031465):0.035132,3:0.032433):0.029883,(4:0.066078,(((5:0.00659,6:0.005689):0.022575,(((7:0.001937,8:1e-06):1e-06,9:0.00252):0.017216,10:0.014062):0.022292):0.081495,((((11:0.002102,12:0.004944):0.00432,(13:0.003012,(14:0.00783,15:0.005824):0.000805):0.00858):0.00704,((16:1e-06,17:1e-06):0.01382,(((((18:0.003691,((19:1e-06,20:1e-06):0.003212,21:0.007451):0.000939):0.003433,((22:1e-06,(23:1e-06,24:1e-06):1e-06):0.009099,((25:0.000972,26:0.003866):0.000478,((27:0.003711,28:0.002171):0.00282,29:0.002886):1e-06):0.003994):0.000465):0.002318,30:0.001986):0.000702,(((31:0.00144,32:0.002891):0.000964,(33:0.002769,((34:0.002553,35:0.001021):0.000492,36:0.002597):2e-06):0.003871):0.006287,((((37:0.000973,38:0.000489):0.002279,39:0.005015):0.001922,(40:1e-06,41:1e-06):0.007105):0.002093,42:0.006841):1e-06):0.000964):0.000499,(((43:0.002424,44:0.002436):0.004367,(((45:0.001723,(46:0.001173,47:0.002208):0.000481):0.002396,(48:0.002941,49:0.004276):0.003268):0.003142,(((50:0.003099,(51:0.00812,52:0.003878):0.001989):0.000993,((53:1e-06,54:1e-06):0.005323,((((55:0.004644,(56:0.003093,57:0.00065):0.001013):0.001287,(58:1e-06,59:1e-06):0.003482):0.001444,60:0.00447):0.000892,(61:0.001447,62:0.001933):1e-06):0.004343):1e-06):0.000496,63:1e-06):1e-06):1e-06):0.001994,((64:0.004424,(65:0.005366,66:0.001469):1e-06):0.003375,((67:0.00288,68:0.007836):0.006363,(69:0.00097,((((70:0.000962,(71:1e-06,72:1e-06):0.000961):0.000481,(73:1e-06,(74:1e-06,75:0.001673):1e-06):0.001796):1e-06,(76:0.002889,77:0.001445):1e-06):0.000514,78:0.003369):0.000505):0.005587):1e-06):0.001014):0.002384):0.003864):0.003769):0.039697,((((79:0.004867,80:0.00325):0.008655,((81:0.002892,82:0.000776):0.005173,83:0.007049):0.005466):0.046206,(84:0.008576,(85:0.009187,86:0.006891):0.000814):0.058813):0.020895,((87:0.004492,(88:0.011162,(89:0.010587,((90:0.007754,((91:0.001779,92:1e-06):0.00283,(93:0.00113,94:0.013844):0.00136):0.005718):0.001823,95:0.006448):0.00099):0.003212):0.002098):0.028662,((((96:0.005311,((97:0.001132,98:0.001135):0.006428,99:1e-06):0.001166):0.001074,(100:0.005169,(101:1e-06,(102:0.00448,103:0.000582):1e-06):0.003161):0.003339):0.039844,(((104:0.05836,((105:0.004525,106:0.00655):0.006397,107:0.003715):0.022655):0.012829,(108:0.000707,(109:0.002601,110:0.003531):0.007472):0.018917):0.01585,(111:0.022189,112:0.023298):0.031873):0.005787):0.09393,(((113:0.033172,(((114:0.012414,(115:0.005637,116:0.005037):0.00885):0.012933,(117:0.017625,118:0.011354):0.002148):0.00025,119:0.026112):0.012042):0.034505,((120:0.012176,(121:0.024877,((122:0.000536,123:0.000559):0.010636,124:0.016276):0.003218):0.011975):0.018538,(125:0.039123,(((126:0.013476,127:0.002148):0.017191,128:0.028731):0.011179,129:0.032877):0.007292):0.007439):0.007158):0.065056,(((130:1e-06,131:1e-06):0.02613,(132:1e-06,133:1e-06):0.010596):0.033234,(134:0.001864,135:0.000544):0.038453):0.019372):0.002816):0.007243):0.003907):0.008444):0.057195):0.091229):0.010136):0.45,136:0.45);
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END;

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