#NEXUS Begin trees; [Treefile saved Fri May 18 23:28:35 2001] [! >Data file = C:\sequenties\embl\embl6B.pau >Heuristic search settings: > Optimality criterion = maximum likelihood > Likelihood settings: > User-specified substitution rate matrix = > - 1.485 3.067 1.723 > 1.485 - 0.9675 3.866 > 3.067 0.9675 - 1 > 1.723 3.866 1 - > Assumed nucleotide frequencies (set by user): > A=0.24120 C=0.19600 G=0.23970 T=0.32310 > Among-site rate variation: > Assumed proportion of invariable sites = 0.1417 > Distribution of rates at variable sites = gamma (discrete > approximation) > Shape parameter (alpha) = 0.6895 > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the GTR+G+I model > Number of distinct data patterns under this model = 1818 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation > method > Trees with approximate likelihoods 5% or further from the target score > are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass > limit=20, delta=1e-006 > -ln L (unconstrained) = unavailable due to missing-data and/or > ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 86400 seconds imposed > Number of rearrangements limited to 5000 > 'MaxTrees' setting = 500 (will not be increased) > Branches collapsed (creating polytomies) if branch length is less than or > equal to 1e-008 > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search terminated by time limit (while swapping on tree #1) > Total number of rearrangements tried = 1871 > Score of best tree(s) found = 64059.50124 > Number of trees retained = 1 > Time used = 24:00:01.0 ] Translate 1 Caenorhabditis_remanei_U13930, 2 Caenorhabditis_elegans_X03680, 3 Caenorhabditis_briggsae_U13929, 4 Caenorhabditis_vulgaris_U13931, 5 unidentified_nematode_U73446, 6 Otostrongylus_sp._U81589, 7 Parafilaroides_sp._U81590, 8 Heterorhabditis_bacteriophora_U70628, 9 Oscheius_sp._U81587, 10 Rhabditella_axei_U13934, 11 Rhabditis_myriophyla_U13936, 12 Pellioditis_typica_U13933, 13 Diploscapter_sp._U81586, 14 Rhabditis_blumi_U13935, 15 Cruznema_tripartitum_U73449, 16 Halicephalobus_gingivalis_AF202156, 17 Panagrolaimus_sp._U81579, 18 Turbatrix_aceti_AF202165, 19 Plectonchus_sp._AF202154, 20 Panagrobelus_stammeri_AF202153, 21 Strongyloides_rattiKT_U81581, 22 Strongyloides_stercoralis_M84229, 23 Rhabditophanes_sp._AF202151, 24 panagrolaimoid_nematode_U81580, 25 Aduncospiculum_halicti_U61759, 26 Diplogaster_lethieri_AF036643, 27 Pristionchus_lheritieri_AF036640, 28 Pristionchus_pacificus_U81584, 29 Teratorhabditis_palmarum_U13937, 30 Mesorhabditis_sp._U73452, 31 Bunonema_sp._U81582, 32 Pelodera_strongyloides_U13932, 33 Bursaphelenchus_sp._AF037369, 34 Brevibuca_sp._AF202163, 35 Parascaris_equorum_U94378, 36 Ascaris_suum_U94367, 37 Ascaris_lumbricoides_U94366, 38 Baylisascaris_procyonis_U94368, 39 Baylisascaris_transfuga_U94369, 40 Toxascaris_leonina_U94383, 41 Porrocaecum_depressum_U94379, 42 Toxocara_canis_U94382, 43 Contracaecum_multipapillatum_U94370, 44 Pseudoterranova_decipiens_U94380, 45 Anisakis_sp._U94365, 46 Anisakis_sp._U81575, 47 Terranova_caballeroi_U94381, 48 Goezia_pelagia_U94372, 49 Iheringascaris_inquies_U94377, 50 Hysterothylacium_pelagicum_U94375, 51 Hysterothylacium_fortalezae_U94374, 52 Hysterothylacium_reliquens_U94376, 53 Cruzia_americana_U94371, 54 Heterocheilus_tunicatus_U94373, 55 Wuchereria_bancrofti_AF227234, 56 Philonema_sp._U81574, 57 Litomosoides_sigmodontis_AF227233, 58 Dirofilaria_immitis_AF036638, 59 Gnathostoma_binucleatum_Z96946, 60 Gnathostoma_neoprocyonis_Z96947, 61 Gnathostoma_turgidum_Z96948, 62 Tylocephalus_auriculatus_AF202155, 63 Plectus_minimus_U61761, 64 Plectus_acuminatus_AF037628, 65 Myolaimus_sp._U81585, 66 Acrobeloides_bodenheimeri_AF202159, 67 Acrobeloides_bodenheimeri_AF202162, 68 Pseudacrobeles_variabilis_AF202150, 69 Cephalobus_sp._AF202158, 70 Cephalobus_sp._AF202160, 71 Cephalobus_oryzae_AF034390, 72 Acrobeloides_sp._AF034391, 73 Cervidellus_alutus_AF202152, 74 Acrobeles_sp._U81576, 75 Seleborca_complexa_U81577, 76 Acrobeles_ciliatus_AF202148, 77 Zeldia_punctata_U61760, 78 Cephalobus_cubaensis_AF202161, 79 Meloidogyne_arenaria_U42342, 80 Meloidogyne_incognitaKT_U81578, 81 Pratylenchoides_magnicauda_AF202157, 82 Subanguina_radicicola_AF202164, 83 Cuticularia_sp._U81583, 84 Cylindrolaimus_sp._AF202149, 85 Daptonema_procerus_AF047889, 86 Diplolaimelloides_meyli_AF036644, 87 Stilbonema_majum_Y16922, 88 Leptonemella_sp._Y16920, 89 Laxus_cosmopolitus_Y16918, 90 Laxus_oneistus_Y16919, 91 Catanema_sp._Y16912, 92 Eubostrichus_dianae_Y16915, 93 Eubostrichus_parasitiferus_Y16916, 94 Eubostrichus_topiarius_Y16917, 95 Robbea_hypermnestra_Y16921, 96 Desmodora_ovigera_Y16913, 97 Chromadoropsis_vivipara_AF047891, 98 Xyzzors_sp._Y16923, 99 Acanthopharynx_micans_Y16911, 100 Paracanthonchus_caecus_AF047888, 101 Enoplus_meridionalis_Y16914, 102 Enoplus_brevis_U88336, 103 Adoncholaimus_sp._AF036642, 104 Pontonema_vulgare_AF047890, 105 Trichuris_muris_AF036637, 106 Trichinella_spiralis_U60231, 107 Mermis_nigrescens_AF036641, 108 Priapulus_caudatus, 109 Pristionchus_pacificus_AF083010, 110 Pelodera_punctata_AF083018, 111 Paraspidodera_sp._AF083005, 112 Heterakis_sp._AF083003, 113 Rhabditoides_inermiformis_AF083017, 114 Poikilolaimus_regenfussi_AF083022, 115 Poikilolaimus_oxycerca_AF083023, 116 Oscheius_sp._AF082994, 117 Oscheius_insectivora_AF083019, 118 Pellioditis_marina_AF083021, 119 Pellioditis_mediterranea_AF083020, 120 Rhabditella_sp._AF083000, 121 Heterorhabditis_hepialus_AF083004, 122 Oscheius_sp._AF082995, 123 Oscheius_dolichuroides_AF082998, 124 Rhabditis_sp._AF083008, 125 Cephaloboides_sp._AF083027, 126 Choriorhabditis_dudichi_AF083012, 127 Caenorhabditis_sonorae_AF083026, 128 Caenorhabditis_drosophilae_AF083025, 129 Caenorhabditis_sp._AF083006, 130 Rhabditoides_inermis_AF082996, 131 Diploscapter_sp._AF083009, 132 Protorhabditis_sp._AF083024, 133 Protorhabditis_sp._AF083001, 134 Rhabditoides_regina_AF082997, 135 Crustorhabditis_scanica_AF083014, 136 Parasitorhabditis_sp._AF083028, 137 Distolabrellus_veechi_AF082999, 138 Distolabrellus_veechi_AF083011, 139 Teratorhabditis_synpapillata_AF083015, 140 Mesorhabditis_spiculigera_AF083016, 141 Mesorhabditis_anisomorpha_AF083013, 142 Pelodera_teres_AF083002, 143 Panagrellus_redivivus_AF083007 ; tree PAUP_1 = [&R] ((((((((((((((((((((((1:0.0,2:0.0):0.0,(3:0.0,4:0.0):0.0):0.1,5:0.0):0.0,129:0.0):0.1,128:0.1):0.1,127:0.1):0.0,(((((6:0.0,7:0.0):0.1,(8:0.0,121:0.0):0.0):0.0,(((((9:0.1,(122:0.0,123:0.0):0.1):0.1,(11:0.0,(116:0.0,117:0.1):0.0):0.0):0.0,((10:0.0,(120:0.0,125:0.2):0.0):0.1,(14:0.2,124:0.1):0.1):0.0):0.0,12:0.6):0.0,(118:0.0,119:0.1):0.0):0.0):0.0,15:0.2):0.0,126:0.2):0.0):0.0,(((13:0.1,131:0.0):0.1,132:0.1):0.1,133:0.3):0.1):0.2,((((((29:0.1,139:0.0):0.1,((((30:0.1,141:0.2):0.0,140:0.1):0.0,136:0.1):0.0,135:0.1):0.0):0.0,(137:0.0,138:0.0):0.1):0.1,134:0.2):0.0,142:0.7):0.0,(32:0.3,110:0.2):1.7):0.1):0.0,((25:0.2,((26:0.0,27:0.0):0.0,(28:0.0,109:0.1):0.0):0.2):0.1,130:0.3):0.0):0.0,31:0.4):0.0,((83:0.1,115:0.0):0.0,114:0.0):0.1):0.0,113:0.1):0.0,65:0.2):0.0,(((((((((16:0.6,18:0.3):0.1,17:0.2):0.0,143:0.3):0.1,(19:0.1,20:0.0):0.1):0.2,((21:0.1,22:0.1):0.2,(23:0,24:0.0):0.1):0.5):0.1,(((((((66:0.0,67:0.0):0.0,(68:0.0,((73:0.0,76:0.0):0.0,(74:0.0,75:0.0):0.0):0.0):0.0):0.0,72:0.0):0.0,((69:0.0,71:0):0.0,70:0.0):0.0):0.0,78:0.1):0.0,77:0.0):0.1,(((79:0.0,80:0.0):0.2,81:0.0):0.0,82:0.1):0.1):0.0):0.0,33:0.5):0.1,34:0.4):0.0,(((((((((((35:0.0,36:0.0):0.0,37:0.0):0.0,(38:0,39:0.0):0.0):0.0,40:0.0):0.0,41:0.0,(42:0.0,43:0.0):0.0):0.0,(48:0.0,((49:0.0,50:0.0):0.0,(51:0.0,52:0.0):0.0):0.0):0.0):0.0,(((44:0,46:0.0):0.0,45:0.0):0.0,47:0.0):0.0):0.0,54:0.0):0.0,(53:0.0,(111:0.0,112:0.1):0.0):0.0):0.0,(((55:0.0,58:0.1):0.0,57:0.1):0.0,56:0.1):0.0):0.0,((59:0.0,61:0.0):0.0,60:0.0):0.1):0.0):0.0):0.0,(62:0.0,(63:0.0,64:0.0):0.0):0.1):0.1,84:0.1):0.0,(85:0.2,86:0.3):0.1):0.1,(((((87:0.0,(92:0.1,(93:0.0,94:0.0):0.0):0.0):0.0,88:0.1):0.0,((89:0.0,90:0.0):0.0,91:0.1):0.0):0.0,95:0.1):0.0,(((96:0.1,97:0.1):0.0,98:0.1):0.0,99:0.1):0.0):0.1):0.0,100:0.1):0.0,((101:0.1,102:0.0):0.1,(103:0.1,104:0.1):0.2):0.0):0.0,((105:0.4,106:0.1):0.1,107:0.2):0.1,108:0.2); End;