initial_explor.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "By johaGL 2021  "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [],
   "source": [
    "from Bio import Phylo"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [],
   "source": [
    "p = Phylo.parse('tiny.map','newick')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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      "                                                            Clade(branch_length=0.784347, name='A')\n",
      "                                                                Clade(branch_length=0.168145, name='A')\n",
      "                                                                    Clade(branch_length=2.24586, name='A')\n",
      "                                                                    Clade(branch_length=0.207214, name='A')\n",
      "                                                                Clade(branch_length=0.590197, name='A')\n",
      "                                                            Clade(branch_length=1.65689, name='A')\n",
      "                                                        Clade(branch_length=0.315045, name='A')\n",
      "                                                            Clade(branch_length=0.185397, name='A')\n",
      "                                                                Clade(branch_length=2.20216, name='A')\n",
      "                                                                    Clade(branch_length=0.193712, name='A')\n",
      "                                                                    Clade(branch_length=2.09929, name='A')\n",
      "                                                                Clade(branch_length=0.55802, name='A')\n",
      "                                                            Clade(branch_length=1.71971, name='A')\n",
      "                                                    Clade(branch_length=0.786664, name='A')\n",
      "                                                Clade(branch_length=0.0676901, name='A')\n",
      "                                            Clade(branch_length=0.940494, name='A')\n",
      "                                                Clade(branch_length=0.943277, name='A')\n",
      "                                                    Clade(branch_length=0.39336, name='A')\n",
      "                                                        Clade(branch_length=0.179769, name='A')\n",
      "                                                        Clade(branch_length=0.732066, name='A')\n",
      "                                                            Clade(branch_length=0.258611, name='A')\n",
      "                                                            Clade(branch_length=1.12439, name='A')\n",
      "                                                    Clade(branch_length=0.873607, name='A')\n",
      "                                                        Clade(branch_length=0.831612, name='A')\n",
      "                                                            Clade(branch_length=5.7511, name='A')\n",
      "                                                            Clade(branch_length=0.000324848, name='A')\n",
      "                                                        Clade(branch_length=0.32383, name='A')\n",
      "                                                Clade(branch_length=0.046498, name='A')\n",
      "                                                    Clade(branch_length=0.2522, name='A')\n",
      "                                                    Clade(branch_length=0.951152, name='A')\n",
      "                                    Clade(branch_length=0.479996, name='A')\n",
      "                                        Clade(branch_length=0.159082, name='A')\n",
      "                                            Clade(branch_length=0.645808, name='A')\n",
      "                                            Clade(branch_length=0.75654, name='A')\n",
      "                                                Clade(branch_length=0.276299, name='A')\n",
      "                                                Clade(branch_length=0.267234, name='A')\n",
      "                                        Clade(branch_length=0.670735, name='A')\n",
      "                                            Clade(branch_length=1.14113, name='A')\n",
      "                                                Clade(branch_length=0.427512, name='A')\n",
      "                                                    Clade(branch_length=0.770698, name='A')\n",
      "                                                    Clade(branch_length=0.581217, name='A')\n",
      "                                                Clade(branch_length=0.145319, name='A')\n",
      "                                                    Clade(branch_length=0.778751, name='A')\n",
      "                                                    Clade(branch_length=0.0829025, name='A')\n",
      "                                            Clade(branch_length=0.392815, name='A')\n",
      "                        Clade(branch_length=0.131764, name='A')\n",
      "                            Clade(branch_length=1.11449, name='A')\n",
      "                            Clade(branch_length=0.551144, name='A')\n",
      "                    Clade(branch_length=0.241861, name='C')\n",
      "                Clade(branch_length=1.5523, name='A')\n",
      "                    Clade(branch_length=2.36365, name='A')\n",
      "                        Clade(branch_length=0.229449, name='A')\n",
      "                            Clade(branch_length=0.335094, name='A')\n",
      "                                Clade(branch_length=1.81297, name='A')\n",
      "                                Clade(branch_length=1.59974, name='A')\n",
      "                                    Clade(branch_length=1.14771, name='A')\n",
      "                                        Clade(branch_length=0.340702, name='A')\n",
      "                                        Clade(branch_length=0.550216, name='A')\n",
      "                                    Clade(branch_length=0.142509, name='A')\n",
      "                            Clade(branch_length=0.384333, name='A')\n",
      "                        Clade(branch_length=0.0558738, name='A')\n",
      "                            Clade(branch_length=1.37603, name='A')\n",
      "                            Clade(branch_length=0.0374298, name='A')\n",
      "                    Clade(branch_length=0.0475451, name='A')\n",
      "                        Clade(branch_length=0.567342, name='A')\n",
      "                            Clade(branch_length=0.123452, name='A')\n",
      "                            Clade(branch_length=0.0438411, name='A')\n",
      "                        Clade(branch_length=1.28641, name='A')\n",
      "        Clade(branch_length=0.140834, name='A')\n",
      "            Clade(branch_length=0.642914, name='A')\n",
      "                Clade(branch_length=1.33634, name='A')\n",
      "                    Clade(branch_length=0.350045, name='A')\n",
      "                        Clade(branch_length=0.223508, name='A')\n",
      "                            Clade(branch_length=0.346799, name='A')\n",
      "                            Clade(branch_length=0.0114686, name='A')\n",
      "                        Clade(branch_length=0.776254, name='A')\n",
      "                            Clade(branch_length=0.110861, name='A')\n",
      "                            Clade(branch_length=2.04635, name='A')\n",
      "                    Clade(branch_length=0.974896, name='A')\n",
      "                        Clade(branch_length=0.254817, name='A')\n",
      "                            Clade(branch_length=0.152334, name='C')\n",
      "                                Clade(branch_length=0.314096, name='A')\n",
      "                                Clade(branch_length=0.261089, name='A')\n",
      "                            Clade(branch_length=0.10942, name='C')\n",
      "                                Clade(branch_length=0.11455, name='A')\n",
      "                                    Clade(branch_length=0.36193, name='A')\n",
      "                                    Clade(branch_length=0.415983, name='A')\n",
      "                                Clade(branch_length=0.245401, name='A')\n",
      "                        Clade(branch_length=0.0869435, name='A')\n",
      "                Clade(branch_length=0.0956085, name='A')\n",
      "                    Clade(branch_length=0.552875, name='A')\n",
      "                        Clade(branch_length=1.31876, name='A')\n",
      "                        Clade(branch_length=0.361975, name='A')\n",
      "                    Clade(branch_length=0.335487, name='A')\n",
      "            Clade(branch_length=0.797841, name='A')\n",
      "        Clade(branch_length=0.415931, name='A')\n"
     ]
    }
   ],
   "source": [
    "for t in p:\n",
    "    print(t)\n",
    "    "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "As we see,this do not help because this do not shows the mutations on each branch, only curent nucleotide . I did not find any biopython function allowing to do so."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open('tiny.map', 'r') as file:\n",
    "    trees = file.readlines()\n",
    "l_t = []\n",
    "for i in trees:\n",
    "    l_t.append(i.strip())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['((((((Pseudomonas_aeruginosa_0C2E_A:0.849361:A:0.457946:C:0.877233:A:0.144661:C:0.227243:A,(Pseudomonas_aeruginosa_CF18_A:0.16136:A,Pseudomonas_aeruginosa_19660_C:0.239681:C:1.12322:A)_A:0.678396:A)_A:0.426088:A,Pseudomonas_sp_HMSC066A08_A:0.923202:A)_A:0.44525:A,Pseudomonas_aeruginosa_PA7_A:0.0765058:A)_A:0.950755:A,((Pseudomonas_sp_57B_090624_A:0.26534:A,(Pseudomonas_sp_FeS53a_A:1.21988:A,(Pseudomonas_sp_1D4_A:1.21752:A,Pseudomonas_sp_ENNP23_A:0.208598:A:0.0351748:C:0.341391:A)_A:0.812451:A:0.0523931:C:2.99696:A)_A:0.0152426:A)_A:0.605998:A,(Pseudomonas_sp_DY_1_A:0.516202:A,Pseudomonas_furukawaii_A:1.22359:A)_A:0.161995:A)_A:0.0104311:A)_A:0.383539:A,((((((((Pseudomonas_alkylphenolica_A:1.12159:A,Pseudomonas_sp_1033_A:1.2702:A:0.367922:C:0.0895452:A)_A:0.231803:A:0.145122:C:0.0800722:A,Pseudomonas_sp_SDI_A:0.611623:A)_A:1.14613:A,((((Pseudomonas_capeferrum_A:0.177741:A,((((Pseudomonas_entomophila_C:0.0270728:C:0.0467763:A:0.0591214:C:0.3473:A,((((Pseudomonas_sp_DP16D_E2_A:0.215619:A,Pseudomonas_sp_2848_A:1.33995:A)_A:0.971418:A,Pseudomonas_soli_A:0.0185445:A)_A:1.50023:A,Pseudomonas_sp_CCOS_191_A:0.708461:A)_A:0.267515:A,(Pseudomonas_sp_DrBHI1_A:1.63612:A,Pseudomonas_sp_250J_A:0.751697:A)_A:0.490792:A)_A:1.20677:A)_A:0.0882079:A,Pseudomonas_sp_RIT623_A:0.764092:A)_A:0.0764645:A,((((Pseudomonas_plecoglossicida_A:0.234811:A:0.0177791:C:0.738591:A,Pseudomonas_sp_GM84_A:1.07564:A)_A:0.115456:A,(Pseudomonas_putida_W619_A:0.505203:A,Pseudomonas_sp_p106_A:0.000751523:A)_A:0.217037:A)_A:1.54044:A,(((((((((Pseudomonas_putida_A:0.142332:A,Pseudomonas_sp_SWI36_A:0.3813:A)_A:0.928124:A,(Pseudomonas_hunanensis_A:0.209117:A,Pseudomonas_putida_BIRD_1_A:0.583912:A)_A:0.521426:A)_A:0.111236:A,Pseudomonas_putida_LF54_A:0.477188:A)_A:0.0491992:A,Pseudomonas_putida_GB_1_A:1.37175:A:0.100486:C:0.37273:A)_A:1.55422:A,Pseudomonas_sp_10_1B_A:0.762994:A)_A:0.788613:A,(Pseudomonas_sp_LB_090624_A:0.305601:A:0.13956:C:0.113662:A,(Pseudomonas_sp_LLC_1_A:0.563375:A,Pseudomonas_sp_LTGT_11_2Z_A:0.0490223:A)_A:1.17761:A)_A:0.437853:A)_A:0.333175:A,(((Pseudomonas_putida_H8234_A:0.00345976:A,Pseudomonas_putida_S1312_A:0.0658104:A)_A:0.87367:A:0.212785:C:0.282991:A,Pseudomonas_putida_NBRC_14164_A:0.370206:A)_A:0.759969:A:0.0545511:C:0.296328:A,Pseudomonas_sp_Leaf58_A:0.199013:A)_A:0.687835:A:0.0360527:C:1.12917:A)_A:0.035227:A:0.217125:C:0.244196:A,(((((Pseudomonas_putida_KG_4_A:0.0702313:A,Pseudomonas_sp_FGI182_A:1.17823:A)_A:0.716435:A,Pseudomonas_sp_C5pp_A:0.246657:A)_A:0.0896187:A,((Pseudomonas_putida_S16_A:0.378713:A,Pseudomonas_monteilii_SB3078_A:0.230361:A)_A:0.442033:A:0.181179:C:0.576396:A,Pseudomonas_sp_ABFPK_A:0.460153:A)_A:0.373314:A)_A:0.420401:A,Pseudomonas_putida_HB3267_A:0.163071:A)_A:0.717645:A,Pseudomonas_sp_AFG_SD02_1510_Pfu_092_A:1.52493:A:0.0504222:C:0.691533:A)_A:0.744075:A)_A:2.4376:A,((Pseudomonas_sp_LP_4_YM_A:0.338209:A,Pseudomonas_putida_S610_A:0.0314291:A)_A:1.06979:A,Pseudomonas_sp_SGAir0191_A:0.211357:A)_A:0.682101:A)_A:1.44905:A)_A:0.575251:A,(Pseudomonas_sp_CC120222_01a_A:0.423756:A,Pseudomonas_sp_382_A:0.191673:A)_A:0.789656:A)_A:0.269818:A)_A:0.9898:A,(Pseudomonas_guariconensis_A:0.600768:A:0.00855261:C:1.03997:A,Pseudomonas_sp_HMSC08G10_A:1.17287:A)_A:0.60395:A)_A:0.627477:A)_A:0.0942264:A,(Pseudomonas_reidholzensis_A:0.0418173:A,Pseudomonas_sp_02C_26_A:0.577718:A)_A:0.0755264:A:0.051358:C:1.08193:A)_A:0.0644242:A:0.00676364:C:0.489543:A,Pseudomonas_putida_CSV86_A:0.0930397:A)_A:1.00782:A,Pseudomonas_sp_FFUP_PS_473_A:0.0497237:A)_A:1.63225:A)_A:0.736799:A,(((Pseudomonas_coleopterorum_A:0.309608:A,(Pseudomonas_sp_RIT_PI_a_A:0.85752:A,Pseudomonas_sp_Leaf129_A:0.462946:A)_A:0.284322:A)_A:0.0667823:A,Pseudomonas_rhizosphaerae_A:1.79885:A)_A:0.289251:A:0.108047:C:1.4234:A,Pseudomonas_sp_M47T1_A:0.903602:A)_A:1.39607:A)_A:3.15141:A,(((((((((((Pseudomonas_amygdali_pv_mellea_A:0.329846:A,Pseudomonas_sp_ICMP_3272_A:0.672731:A)_A:0.0759497:A,((Pseudomonas_amygdali_pv_hibisci_A:0.0621623:A,Pseudomonas_ficuserectae_A:0.624062:A)_A:0.629887:A,Pseudomonas_amygdali_pv_sesami_A:0.419116:A)_A:0.0248208:A)_A:0.00587112:A,Pseudomonas_syringae_pv_broussonetiae_A:0.587112:A:0.0747923:C:0.300341:A)_A:0.890065:A,Pseudomonas_amygdali_pv_mori_A:0.642199:A)_A:0.272184:A,(Pseudomonas_congelans_A:0.226629:A,((((Pseudomonas_syringae_BRIP34876_A:0.0490159:A,Pseudomonas_syringae_ICMP_11168_A:0.135825:A)_A:1.65065:A,Pseudomonas_syringae_pv_avellanae_str_ISPaVe037_A:0.476881:A)_A:0.127994:A,Pseudomonas_cerasi_A:0.460581:A)_A:0.843093:A,(Pseudomonas_caricapapayae_A:0.255573:A,Pseudomonas_syringae_pv_tagetis_C:0.0478441:C:1.0702:A)_A:0.117706:A:0.0024695:C:0.128941:A)_A:0.737951:A)_A:0.290523:A)_A:1.40194:A,(((((Pseudomonas_amygdali_pv_morsprunorum_A:1.01889:A,Pseudomonas_avellanae_BPIC_631_A:2.72385:A)_A:0.142411:A,(Pseudomonas_syringae_pv_theae_ICMP_3923_C:0.041318:C:0.0210384:A,Pseudomonas_syringae_pv_actinidiae_A:1.08119:A)_A:0.166945:A)_A:1.45064:A,Pseudomonas_syringae_pv_apii_A:0.261555:A)_A:0.483612:A,((Pseudomonas_syringae_pv_syri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      ]
     },
     "execution_count": 38,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "trees"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       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M48_A:1.84662:A,Pseudomonas_sp_GM74_A:0.640569:A)_A:0.609463:A:0.0712442:C:0.278335:A)_A:1.22449:A:0.0780868:C:0.457565:A)_A:0.994918:A,Pseudomonas_sp_GV085_A:0.752888:A)_A:0.392617:A,((Pseudomonas_sp_B12018_A:0.545083:A,Pseudomonas_sp_GM33_A:0.286885:A)_A:0.218699:A,((Pseudomonas_sp_GW456_E7_A:0.456366:A,Pseudomonas_sp_ACN5_A:0.358941:A)_A:0.460763:A,Pseudomonas_sp_UW4_A:0.250844:A)_A:0.666169:A)_A:0.160687:A)_A:0.0728284:A,(Pseudomonas_sp_LAB_08_A:1.59332:A,Pseudomonas_vancouverensis_C:0.00734097:C:2.67194:A)_A:0.787052:A)_A:0.259172:A,Pseudomonas_sp_GM55_A:1.06034:A)_A:0.13404:A,((Pseudomonas_sp_GM78_A:2.22355:A,Pseudomonas_sp_OV529_A:0.522182:A)_A:2.85919:A:0.143682:C:0.49019:A,Pseudomonas_sp_MYb115_A:0.64909:A)_A:1.89064:A)_A:0.652615:A:0.0754341:C:0.0655126:A,Pseudomonas_sp_Leaf48_A:0.174617:A)_A:0.380556:A,(Pseudomonas_reinekei_A:0.818588:A,Pseudomonas_sp_Root562_A:0.466025:A)_A:0.357594:A:0.307539:C:1.782:A)_A:0.175095:A,(Pseudomonas_mohnii_A:1.19287:A,Pseudomonas_moorei_A:0.549448:A)_A:0.486343:A)_A:1.12122:A)_A:0.0118715:A)_A:0.200874:A,((((((Pseudomonas_fluorescens_F113_C:0.0209505:C,(Pseudomonas_sp_NFACC05_1_A:0.404272:A,Pseudomonas_sp_Root401_A:0.214831:A)_A:0.487526:A:0.391218:C)_C:0.0326601:C:1.16805:A,Pseudomonas_sp_A252017_A:0.942786:A)_A:0.455263:A,(((Pseudomonas_fluorescens_Q2_87_A:0.302304:A,Pseudomonas_frederiksbergensis_A:1.278:A)_A:0.594758:A,((Pseudomonas_sp_MPBD7_1_A:0.488828:A,((((Pseudomonas_sp_NFACC11_2_A:0.981965:A,Pseudomonas_sp_NFACC52_A:0.149088:A)_A:0.146909:A,Pseudomonas_sp_NFACC06_1_A:0.472924:A:0.162253:C:0.446102:A)_A:1.28315:A,Pseudomonas_sp_NFACC13_1_A:0.525538:A)_A:0.314371:A,Pseudomonas_sp_NFACC04_2_A:0.336267:A)_A:0.234512:A)_A:1.2909:A:0.145345:C:0.836537:A,Pseudomonas_sp_NFACC24_1_A:0.835013:A)_A:0.204474:A)_A:0.279264:A,Pseudomonas_sp_43mfcvi11_A:2.98676:A)_A:0.0975545:A)_A:1.906:A,Pseudomonas_sp_11K1_A:0.0686461:A)_A:3.67333:A,(Pseudomonas_sp_A214_A:0.49999:A,(Pseudomonas_sp_NFACC39_1_A:0.683508:A,Pseudomonas_sp_NFACC45_A:0.0920263:A)_A:0.0333053:A)_A:0.468351:A)_A:0.630463:A:0.0143524:C:0.221687:A:0.0830487:C:0.130231:A,((Pseudomonas_mediterranea_A:1.18686:A:0.077738:C:0.296345:A,Pseudomonas_sp_7SR1_A:0.125875:A:0.0481334:C:0.248867:A)_A:0.44643:A:0.060733:C:0.448871:A,Pseudomonas_sp_MWU13_2860_A:0.0141831:A)_A:0.026305:A)_A:0.386623:A)_A:0.0425484:A,(((((((Pseudomonas_chlororaphis_O6_A:2.24586:A,Pseudomonas_sp_RW409_A:0.164858:A:0.0778564:C:0.207214:A)_A:0.224567:A:0.0106899:C:0.168145:A,Pseudomonas_chlororaphis_subsp_aurantiaca_A:0.590197:A)_A:0.784347:A,Pseudomonas_sp_FW306_2_2C_D06C_A:0.0689557:A:0.118586:C:1.65689:A)_A:0.535933:A,(((Pseudomonas_chlororaphis_subsp_aureofaciens_30_84_A:0.193712:A,Pseudomonas_sp_NFPP07_A:2.09929:A)_A:2.20216:A,Pseudomonas_sp_09C_129_A:0.55802:A)_A:0.185397:A,Pseudomonas_sp_FW126_L8_A:1.71971:A)_A:0.315045:A)_A:0.0885251:A,Pseudomonas_sp_NFIX28_A:0.786664:A)_A:0.15265:A,Pseudomonas_sp_MRSN12121_A:0.0676901:A)_A:0.787556:A,(((Pseudomonas_protegens_A:0.179769:A,(Pseudomonas_protegens_CHA0_A:0.0277097:A:0.0588971:C:0.258611:A,Pseudomonas_sp_NFPP05_A:1.12439:A)_A:0.732066:A)_A:0.39336:A,((Pseudomonas_saponiphila_A:5.7511:A,Pseudomonas_sp_Os17_A:0.000324848:A)_A:0.831612:A,Pseudomonas_sp_MWU12_2534b_A:0.32383:A)_A:0.873607:A)_A:0.943277:A,(Pseudomonas_sp_CMR12a_A:0.2522:A,Pseudomonas_sp_FW507_12TSA_A:0.951152:A)_A:0.046498:A)_A:0.940494:A)_A:0.0082827:A)_A:0.0137904:A,((Pseudomonas_lutea_A:0.645808:A,(Pseudomonas_graminis_A:0.276299:A,Pseudomonas_sp_GV012_A:0.267234:A)_A:0.75654:A)_A:0.159082:A,(((Pseudomonas_sp_NFACC02_A:0.770698:A,Pseudomonas_sp_NFR16_A:0.581217:A)_A:0.427512:A,(Pseudomonas_sp_Bc_h_A:0.778751:A,Pseudomonas_sp_RIT_409_A:0.0829025:A)_A:0.145319:A)_A:1.14113:A,Pseudomonas_sp_LP_7_YM_A:0.392815:A)_A:0.670735:A)_A:0.479996:A)_A:0.150431:A)_A:0.4566:A)_A:1.27439:A,(Pseudomonas_sp_GV034_A:1.11449:A,Pseudomonas_sp_K1S02_6_A:0.551144:A)_A:0.131764:A)_A:0.264346:A:0.457542:C,Pseudomonas_cuatrocienegasensis_A:0.257122:A:0.241861:C)_C:0.322696:C:0.181732:A,((((Pseudomonas_fulva_12_X_A:1.81297:A,((Pseudomonas_sp_PA12017_A:0.340702:A,Pseudomonas_sp_PA272017_A:0.550216:A)_A:1.14771:A,Pseudomonas_sp_PA152017_A:0.142509:A)_A:1.59974:A)_A:0.335094:A,Pseudomonas_straminea_A:0.384333:A)_A:0.229449:A,(Pseudomonas_punonensis_A:1.37603:A,Pseudomonas_sp_P18A_A:0.0374298:A)_A:0.0558738:A)_A:2.36365:A,((Pseudomonas_sp_YY_1_A:0.123452:A,Pseudomonas_sp_PI11_A:0.0438411:A)_A:0.567342:A,Pseudomonas_composti_A:0.0550557:A:0.351402:C:0.173211:A:0.0271012:C:1.28641:A)_A:0.0475451:A)_A:1.5523:A)_A:0.106356:A)_A:1.06825:A,(((((Pseudomonas_songnenensis_A:0.346799:A,Pseudomonas_sp_CO183_A:0.0114686:A)_A:0.223508:A,(Pseudomonas_sp_TTU2014_105ASC_A:0.324306:A:0.163581:C:0.110861:A,Pseudomonas_stutzeri_ATCC_14405___CCUG_16156_A:2.04635:A)_A:0.776254:A)_A:0.350045:A,(((Pseudomonas_sp_Chol1_A:0.20224:A:0.00169942:C:0.314096:A,Pseudomonas_sp_HMP271_A:0.261089:A)_A:1.37272:A:0.152334:C,((Pseudomonas_sp_R2A2_A:0.36193:A,Pseudomonas_stutzeri_ATCC_17588___LMG_11199_A:0.415983:A)_A:0.11455:A,Pseudomonas_stutzeri_B1SMN1_A:2.35763:A:0.361567:C:0.245401:A)_A:0.845517:A:0.10942:C)_C:0.0638304:C:0.254817:A,Pseudomonas_stutzeri_NF13_A:0.0869435:A)_A:0.974896:A)_A:1.33634:A,((Pseudomonas_sp_MT_1_A:1.31876:A,Pseudomonas_xanthomarina_DSM_18231_A:0.361975:A)_A:0.552875:A,Pseudomonas_zhaodongensis_A:0.335487:A)_A:0.0956085:A)_A:0.642914:A,Pseudomonas_sp_PIC25_A:0.797841:A)_A:0.140834:A,Burkholderia_pseudomallei_A:0.415931:A)_A;'"
      ]
     },
     "execution_count": 39,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "l_t[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [],
   "source": [
    "testo = \"(ant:17, (bat:31, cow:22):7, dog:22, (elk:33, fox:12):40);\"\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "      ┌─ant\n",
      "      │     ┌─bat\n",
      "      ├─────┤\n",
      "──────┤     └─cow\n",
      "      ├─dog\n",
      "      │     ┌─elk\n",
      "      └─────┤\n",
      "            └─fox\n"
     ]
    }
   ],
   "source": [
    "from newick import  loads\n",
    "trees = loads(testo)\n",
    "print(trees[0].ascii_art())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [],
   "source": [
    "cool = [n.name for n in trees[0].descendants]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['ant', None, 'dog', None]"
      ]
     },
     "execution_count": 51,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cool"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [
    {
     "ename": "ValueError",
     "evalue": "Node names or branch lengths must not contain \":\"",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-52-4c4db80a2104>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mloco\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mloads\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ml_t\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      2\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mn\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mname\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mloco\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdescendants\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.local/lib/python3.9/site-packages/newick.py\u001b[0m in \u001b[0;36mloads\u001b[0;34m(s, strip_comments, **kw)\u001b[0m\n\u001b[1;32m    373\u001b[0m     \"\"\"\n\u001b[1;32m    374\u001b[0m     \u001b[0mkw\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'strip_comments'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mstrip_comments\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 375\u001b[0;31m     \u001b[0;32mreturn\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mparse_node\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mss\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstrip\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkw\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mss\u001b[0m \u001b[0;32min\u001b[0m \u001b[0ms\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msplit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m';'\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mss\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstrip\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    376\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    377\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.local/lib/python3.9/site-packages/newick.py\u001b[0m in \u001b[0;36m<listcomp>\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m    373\u001b[0m     \"\"\"\n\u001b[1;32m    374\u001b[0m     \u001b[0mkw\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'strip_comments'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mstrip_comments\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 375\u001b[0;31m     \u001b[0;32mreturn\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mparse_node\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mss\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstrip\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkw\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mss\u001b[0m \u001b[0;32min\u001b[0m \u001b[0ms\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msplit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m';'\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mss\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstrip\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    376\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    377\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.local/lib/python3.9/site-packages/newick.py\u001b[0m in \u001b[0;36mparse_node\u001b[0;34m(s, strip_comments, **kw)\u001b[0m\n\u001b[1;32m    483\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mparts\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'('\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    484\u001b[0m             \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'unmatched braces %s'\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mparts\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m100\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 485\u001b[0;31m         \u001b[0mdescendants\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0m_parse_siblings\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m')'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mparts\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkw\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    486\u001b[0m         \u001b[0mlabel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mparts\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    487\u001b[0m     \u001b[0mname\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlength\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcomment\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_parse_name_and_length\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlabel\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.local/lib/python3.9/site-packages/newick.py\u001b[0m in \u001b[0;36m_parse_siblings\u001b[0;34m(s, **kw)\u001b[0m\n\u001b[1;32m    450\u001b[0m     \u001b[0;32mfor\u001b[0m \u001b[0mc\u001b[0m \u001b[0;32min\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0ms\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m\",\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    451\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mc\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m\",\"\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mbracket_level\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;36m0\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0msquare_bracket_level\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 452\u001b[0;31m             \u001b[0;32myield\u001b[0m \u001b[0mparse_node\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"\"\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcurrent\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkw\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    453\u001b[0m             \u001b[0mcurrent\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    454\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
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      "\u001b[0;32m~/.local/lib/python3.9/site-packages/newick.py\u001b[0m in \u001b[0;36mparse_node\u001b[0;34m(s, strip_comments, **kw)\u001b[0m\n\u001b[1;32m    483\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mparts\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstartswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'('\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    484\u001b[0m             \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'unmatched braces %s'\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mparts\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m100\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 485\u001b[0;31m         \u001b[0mdescendants\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0m_parse_siblings\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m')'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mparts\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkw\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    486\u001b[0m         \u001b[0mlabel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mparts\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    487\u001b[0m     \u001b[0mname\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlength\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcomment\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_parse_name_and_length\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlabel\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.local/lib/python3.9/site-packages/newick.py\u001b[0m in \u001b[0;36m_parse_siblings\u001b[0;34m(s, **kw)\u001b[0m\n\u001b[1;32m    450\u001b[0m     \u001b[0;32mfor\u001b[0m \u001b[0mc\u001b[0m \u001b[0;32min\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0ms\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m\",\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    451\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mc\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m\",\"\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mbracket_level\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;36m0\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0msquare_bracket_level\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 452\u001b[0;31m             \u001b[0;32myield\u001b[0m \u001b[0mparse_node\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"\"\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcurrent\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkw\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    453\u001b[0m             \u001b[0mcurrent\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    454\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.local/lib/python3.9/site-packages/newick.py\u001b[0m in \u001b[0;36mparse_node\u001b[0;34m(s, strip_comments, **kw)\u001b[0m\n\u001b[1;32m    486\u001b[0m         \u001b[0mlabel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mparts\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    487\u001b[0m     \u001b[0mname\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlength\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcomment\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_parse_name_and_length\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlabel\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 488\u001b[0;31m     \u001b[0;32mreturn\u001b[0m \u001b[0mNode\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcreate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlength\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mlength\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcomment\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mcomment\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdescendants\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdescendants\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkw\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m~/.local/lib/python3.9/site-packages/newick.py\u001b[0m in \u001b[0;36mcreate\u001b[0;34m(cls, name, length, descendants, comment, **kw)\u001b[0m\n\u001b[1;32m     75\u001b[0m         \u001b[0;34m:\u001b[0m\u001b[0;32mreturn\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;31m \u001b[0m\u001b[0;31m`\u001b[0m\u001b[0mNode\u001b[0m\u001b[0;31m`\u001b[0m \u001b[0minstance\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     76\u001b[0m         \"\"\"\n\u001b[0;32m---> 77\u001b[0;31m         \u001b[0mnode\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcls\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlength\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mlength\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcomment\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mcomment\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkw\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     78\u001b[0m         \u001b[0;32mfor\u001b[0m \u001b[0mdescendant\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mdescendants\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     79\u001b[0m             \u001b[0mnode\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0madd_descendant\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdescendant\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.local/lib/python3.9/site-packages/newick.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, name, length, comment, **kw)\u001b[0m\n\u001b[1;32m     40\u001b[0m         \u001b[0;32mfor\u001b[0m \u001b[0mchar\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mRESERVED_PUNCTUATION\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     41\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mname\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mchar\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mlength\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mchar\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mlength\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 42\u001b[0;31m                 raise ValueError(\n\u001b[0m\u001b[1;32m     43\u001b[0m                     'Node names or branch lengths must not contain \"%s\"' % char)\n\u001b[1;32m     44\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mname\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mValueError\u001b[0m: Node names or branch lengths must not contain \":\""
     ]
    }
   ],
   "source": [
    "loco = loads(l_t[0])\n",
    "print([n.name for n in loco[0].descendants])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
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   "language": "python",
   "name": "python3"
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  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
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