Answers.Body: <p>Okay ... this will probably work</p>
  <pre><code>#NEXUS
  begin trees;
      tree TREE1 = [&amp;R] ((LevantinaFC4779:2.411968,Assyriella_naegelei:2.411968):5.752052,((Cn_IG_1:0.126901,(Cn_IG_2:0.075971,Cn_IG_3:0.075971):0.05093):7.4805,(((CpThe_1:0.122189,CpSka_1:0.122189):2.663216,((CpGio_2:0.137489,(CpGravR6_1:0.087156,(CpGravR3:0.038234,CpGravR4:0.038234):0.048922):0.050334):0.257308,(CpGravR5_1:0.28159,((CpGravR7:0.099712,(CpGravR5_2:0.020255,CpGravR2:0.020255):0.079458):0.15617,(CpGravR6_2:0.109222,(CpGio_1:0.068711,(CpGio_3:0.049345,CpGravR1:0.049345):0.019367):0.040511):0.14666):0.025708):0.113207):2.390607):1.772627,(((Ci_MEN_12:0.072368,(Ci_MEN_1:0.022725,Ci_MEN_2:0.022725):0.049643):1.78894,((CiPLAN2:0.253487,(CiPLAN1:0.067509,CiPLAN3:0.067509):0.185978):0.386279,((Ci_MSP_3:0.061614,Ci_MSP_2:0.061614):0.231268,(Ci_MSP_1:0.113777,(Ci_DIA_1:0.047073,Ci_DIA_2:0.047073):0.066704):0.179105):0.346885):1.221542):1.580745,(((Ceu_LAG_2:1.580984,(CeuMist2:0.198982,CeuMist1:0.198982):1.382002):0.341226,((Ceu_PAN_2:0.046898,Ceu_PAN_1:0.046898):0.20368,(Ceu_PAN_3:0.018814,Ceu_PAN_4:0.018814):0.231764):1.671632):1.226475,((CcHr1:1.247104,((CcRod1:0.403751,(CcRod4:0.276104,(CcRod2:0.158977,CcRod3:0.158977):0.117127):0.127647):0.308704,((Cc_Mal_1:0.138232,Cc_KalR2_2:0.138232):0.395435,(CcMath1:0.338389,(CcNav1:0.091762,CcNav2:0.091762):0.246627):0.195278):0.178788):0.534649):1.609976,(((CeST6_5:0.056918,(CeST6_1:0.030107,CeST6_4:0.030107):0.026812):0.733078,((CeST6_2:0.143014,(CeAA7_1:0.097814,CeST6_3:0.097814):0.0452):0.349431,((Cg_MelR7_1:0.136715,(Cg_MelR3_1:0.088065,(Cg_MelR6_2:0.047987,(Cg_MelR7_2:0.019268,Cg_MelR6_1:0.019268):0.028719):0.040078):0.04865):0.074941,(Cg_MelR5_2:0.143401,(Cg_MelR7_3:0.119131,(Cg_MelR5_1:0.090065,((Cg_MelR4_1:0.020938,Cg_MelR7_4:0.020938):0.051613,(Cg_MelR4_2:0.052913,(Cg_MelR1_1:0.021387,Cg_MelR2_1:0.021387):0.031526):0.019639):0.017514):0.029066):0.02427):0.068255):0.280789):0.297551):0.793423,(((ChTM4_2:0.049871,ChTM5_1:0.049871):0.111934,(ChTM4_3:0.023134,ChTM4_1:0.023134):0.138672):0.228306,(Ch_MEN_9:0.174548,((Ch_MEN_11:0.021817,Ch_MEN_3:0.021817):0.10954,((Ch_MEN_8:0.057141,(Ch_MEN_5:0.022973,Ch_MEN_13:0.022973):0.034168):0.053065,((Ch_LEV_3:0.031056,Ch_LEV_5:0.031056):0.061225,((Ch_LEV_4:0.029359,(Ch_MEN_6:0.017456,Ch_MEN_10:0.017456):0.011904):0.034407,((Ch_LEV_2:0.017911,Ch_MEN_4:0.017911):0.040741,(Ch_MEN_14:0.03419,Ch_LEV_1:0.03419):0.024462):0.005114):0.028515):0.017925):0.021151):0.043191):0.215563):1.193307):1.27366):0.291605):0.293368):1.115978):3.04937):0.556619);
  end;
  </code></pre>
  <p>Alternatively, I'm not sure about the root, just remove <code>[&amp;R]</code> in the above.</p>
  <p>Finally there could be an issue that you haven't obtained the sample directly from the raw Beast output, instead you've summarised it. It might complain about that. Thus it might need all those trees from the raw Beast output. Thats not a format issue it's a data input issue. BayesTraits might be perform the calculation against the total MCMCMC sample minus the burn-in.</p>
  <hr />
  <p>from comments</p>
  <p>Read it into Rs <code>ape::read.nexus()</code> and then write via <code>phytools::writeNexus()</code>. This should produce your translate table. Biopython recognises this format but doesn't write to it.</p>
  <p>The closest Biopython can achieve is a taxablock here</p>
  <pre><code>#NEXUS
  Begin Taxa;
   Dimensions NTax=85;
   TaxLabels LevantinaFC4779 Assyriella_naegelei Cn_IG_1 Cn_IG_2 Cn_IG_3 CpThe_1 CpSka_1 CpGio_2 CpGravR6_1 CpGravR3 CpGravR4 CpGravR5_1 CpGravR7 CpGravR5_2 CpGravR2 CpGravR6_2 CpGio_1 CpGio_3 CpGravR1 Ci_MEN_12 Ci_MEN_1 Ci_MEN_2 CiPLAN2 CiPLAN1 CiPLAN3 Ci_MSP_3 Ci_MSP_2 Ci_MSP_1 Ci_DIA_1 Ci_DIA_2 Ceu_LAG_2 CeuMist2 CeuMist1 Ceu_PAN_2 Ceu_PAN_1 Ceu_PAN_3 Ceu_PAN_4 CcHr1 CcRod1 CcRod4 CcRod2 CcRod3 Cc_Mal_1 Cc_KalR2_2 CcMath1 CcNav1 CcNav2 CeST6_5 CeST6_1 CeST6_4 CeST6_2 CeAA7_1 CeST6_3 Cg_MelR7_1 Cg_MelR3_1 Cg_MelR6_2 Cg_MelR7_2 Cg_MelR6_1 Cg_MelR5_2 Cg_MelR7_3 Cg_MelR5_1 Cg_MelR4_1 Cg_MelR7_4 Cg_MelR4_2 Cg_MelR1_1 Cg_MelR2_1 ChTM4_2 ChTM5_1 ChTM4_3 ChTM4_1 Ch_MEN_9 Ch_MEN_11 Ch_MEN_3 Ch_MEN_8 Ch_MEN_5 Ch_MEN_13 Ch_LEV_3 Ch_LEV_5 Ch_LEV_4 Ch_MEN_6 Ch_MEN_10 Ch_LEV_2 Ch_MEN_4 Ch_MEN_14 Ch_LEV_1;
  End;
  Begin Trees;
   Tree tree1=((LevantinaFC4779:2.41197,Assyriella_naegelei:2.41197):5.75205,((Cn_IG_1:0.12690,(Cn_IG_2:0.07597,Cn_IG_3:0.07597):0.05093):7.48050,(((CpThe_1:0.12219,CpSka_1:0.12219):2.66322,((CpGio_2:0.13749,(CpGravR6_1:0.08716,(CpGravR3:0.03823,CpGravR4:0.03823):0.04892):0.05033):0.25731,(CpGravR5_1:0.28159,((CpGravR7:0.09971,(CpGravR5_2:0.02025,CpGravR2:0.02025):0.07946):0.15617,(CpGravR6_2:0.10922,(CpGio_1:0.06871,(CpGio_3:0.04934,CpGravR1:0.04934):0.01937):0.04051):0.14666):0.02571):0.11321):2.39061):1.77263,(((Ci_MEN_12:0.07237,(Ci_MEN_1:0.02272,Ci_MEN_2:0.02272):0.04964):1.78894,((CiPLAN2:0.25349,(CiPLAN1:0.06751,CiPLAN3:0.06751):0.18598):0.38628,((Ci_MSP_3:0.06161,Ci_MSP_2:0.06161):0.23127,(Ci_MSP_1:0.11378,(Ci_DIA_1:0.04707,Ci_DIA_2:0.04707):0.06670):0.17910):0.34688):1.22154):1.58075,(((Ceu_LAG_2:1.58098,(CeuMist2:0.19898,CeuMist1:0.19898):1.38200):0.34123,((Ceu_PAN_2:0.04690,Ceu_PAN_1:0.04690):0.20368,(Ceu_PAN_3:0.01881,Ceu_PAN_4:0.01881):0.23176):1.67163):1.22647,((CcHr1:1.24710,((CcRod1:0.40375,(CcRod4:0.27610,(CcRod2:0.15898,CcRod3:0.15898):0.11713):0.12765):0.30870,((Cc_Mal_1:0.13823,Cc_KalR2_2:0.13823):0.39543,(CcMath1:0.33839,(CcNav1:0.09176,CcNav2:0.09176):0.24663):0.19528):0.17879):0.53465):1.60998,(((CeST6_5:0.05692,(CeST6_1:0.03011,CeST6_4:0.03011):0.02681):0.73308,((CeST6_2:0.14301,(CeAA7_1:0.09781,CeST6_3:0.09781):0.04520):0.34943,((Cg_MelR7_1:0.13672,(Cg_MelR3_1:0.08807,(Cg_MelR6_2:0.04799,(Cg_MelR7_2:0.01927,Cg_MelR6_1:0.01927):0.02872):0.04008):0.04865):0.07494,(Cg_MelR5_2:0.14340,(Cg_MelR7_3:0.11913,(Cg_MelR5_1:0.09007,((Cg_MelR4_1:0.02094,Cg_MelR7_4:0.02094):0.05161,(Cg_MelR4_2:0.05291,(Cg_MelR1_1:0.02139,Cg_MelR2_1:0.02139):0.03153):0.01964):0.01751):0.02907):0.02427):0.06825):0.28079):0.29755):0.79342,(((ChTM4_2:0.04987,ChTM5_1:0.04987):0.11193,(ChTM4_3:0.02313,ChTM4_1:0.02313):0.13867):0.22831,(Ch_MEN_9:0.17455,((Ch_MEN_11:0.02182,Ch_MEN_3:0.02182):0.10954,((Ch_MEN_8:0.05714,(Ch_MEN_5:0.02297,Ch_MEN_13:0.02297):0.03417):0.05307,((Ch_LEV_3:0.03106,Ch_LEV_5:0.03106):0.06123,((Ch_LEV_4:0.02936,(Ch_MEN_6:0.01746,Ch_MEN_10:0.01746):0.01190):0.03441,((Ch_LEV_2:0.01791,Ch_MEN_4:0.01791):0.04074,(Ch_MEN_14:0.03419,Ch_LEV_1:0.03419):0.02446):0.00511):0.02851):0.01792):0.02115):0.04319):0.21556):1.19331):
  1.27366):0.29161):0.29337):1.11598):3.04937):0.55662):0.00000;
  End;
  </code></pre>
  <p>The solution could be coded from the taxa block if the above doesn't work, but easier to use <strong>R</strong> <code>ape</code> and <code>phytools</code></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-11T12:26:15.040Z
Answers.Text: I tried using this tree you provided as input and got this message: 
  Err: Does have a translate line.
Answers.UserDisplayName: Nickmofoe
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-10T18:05:41.377Z
Answers.LastActivityDate: 2023-10-11T13:45:45.107Z
Answers.LastEditDate: 2023-10-11T13:45:45.107Z
Answers.UserDisplayName: M__
Body: <p>I would like to use the program BayesTraitV4. I have my phylogenetic tree in NEXUS format but the program does not accept it. I checked the example data and while they are also in NEXUS format, they seemed different. I will provide a part of my data and the example data respectively.</p>
  <p>My tree:</p>
  <pre><code>#NEXUS
  begin taxa;
      dimensions ntax=85;
      taxlabels
      LevantinaFC4779
      Assyriella_naegelei
      Ceu_LAG_2
      CeuMist2
      CeuMist1
      Ceu_PAN_2
      Ceu_PAN_1
      Ceu_PAN_3
      Ceu_PAN_4
      CcMath1
      CcNav1
      CcNav2
      Cc_Mal_1
      Cc_KalR2_2
      CcRod1
      CcRod2
      CcRod3
      CcRod4
      CcHr1
      CeST6_1
      CeST6_4
      CeST6_5
      CeAA7_1
      CeST6_3
      CeST6_2
      Cg_MelR7_1
      Cg_MelR3_1
      Cg_MelR6_2
      Cg_MelR7_2
      Cg_MelR6_1
      Cg_MelR7_3
      Cg_MelR5_1
      Cg_MelR4_2
      Cg_MelR1_1
      Cg_MelR2_1
      Cg_MelR4_1
      Cg_MelR7_4
      Cg_MelR5_2
      ChTM4_2
      ChTM5_1
      ChTM4_3
      ChTM4_1
      Ch_MEN_5
      Ch_MEN_13
      Ch_MEN_8
      Ch_LEV_3
      Ch_LEV_5
      Ch_LEV_4
      Ch_MEN_6
      Ch_MEN_10
      Ch_LEV_2
      Ch_MEN_4
      Ch_MEN_14
      Ch_LEV_1
      Ch_MEN_11
      Ch_MEN_3
      Ch_MEN_9
      Ci_MSP_3
      Ci_MSP_2
      Ci_MSP_1
      Ci_DIA_1
      Ci_DIA_2
      CiPLAN1
      CiPLAN3
      CiPLAN2
      Ci_MEN_1
      Ci_MEN_2
      Ci_MEN_12
      CpGravR6_1
      CpGravR3
      CpGravR4
      CpGio_2
      CpGravR5_2
      CpGravR2
      CpGravR7
      CpGio_1
      CpGio_3
      CpGravR1
      CpGravR6_2
      CpGravR5_1
      CpThe_1
      CpSka_1
      Cn_IG_2
      Cn_IG_3
      Cn_IG_1
  ;
  end;
  
  begin trees;
      tree TREE1 = [&amp;R] ((LevantinaFC4779[&amp;rate_range={7.888601174550756E-4,0.2727277039812744},height_95%_HPD={0.0,1.5711876244495215E-12},length_range={0.6843282088933,6.197383612374},height_median=6.004086117172847E-13,length_95%_HPD={1.080900382604,3.875114824373},height=6.614724410322848E-13,rate=0.049900260878735954,height_range={0.0,5.799805080641818E-12},rate_median=0.045084434131968686,length=2.411967820837161,length_median=2.3472043999879997,rate_95%_HPD={0.0108358382756707,0.10141567250363237}]:2.4119678208371664,Assyriella_naegelei[&amp;rate_range={2.4004562386929353E-4,0.19480057878691465},height_95%_HPD={0.0,1.5711876244495215E-12},length_range={0.6843282088933,6.197383612374},height_median=6.004086117172847E-13,length_95%_HPD={1.080900382604,3.875114824373},height=6.614724410322848E-13,rate=0.03027613080757391,height_range={0.0,5.799805080641818E-
  </code></pre>
  <p>Example tree:</p>
  <pre><code>#NEXUS
  Begin trees;
      translate
          1   Opossum,
          2   Diprotodontian,
          3   Sloth,
          4   Armadillo,
          5   Anteater,
          6   Hedgehog,
          7   Mole,
          8   Shrew,
          9   Tenrecid,
          10  Golden_Mole,
          11  Sirenian,
          12  Hyrax,
          13  Elephant,
          15  Lo_Ear_Ele_shrew,
          17  Sciurid,
          18  Mouse,
          19  Rat,
          20  Hystricid,
          21  Caviomorph,
          22  Rabbit,
          23  Pika,
          24  Flying_Lemur,
          25  Tree_Shrew,
          26  Strepsirrhine,
          28  Phyllostomid,
          29  Free_tailed_bat,
          30  False_vampire_bat,
          31  Flying_Fox,
          32  Rousette_Fruitbat,
          33  Whale,
          35  Hippo,
          36  Llama,
          37  Ruminant,
          38  Pig,
          39  Horse,
          40  Rhino,
          41  Tapir,
          42  Cat,
          43  Caniform,
          44  Pangolin;
          tree tree.164000.208997.409491 = ((1:0.07628,2:0.065151):0.1546885,(((15:0.133631,(9:0.157087,10:0.077841):0.007403):0.005959,(11:0.0406,(12:0.092769,13:0.052284):0.001099):0.01453):0.029813,((4:0.05807,(3:0.054688,5:0.062757):0.008238):0.029441,(((26:0.083487,(24:0.064103,25:0.110063):0.003501):0.000775,((22:0.058663,23:0.116805):0.045375,(17:0.0898,((18:0.039267,19:0.043896):0.125808,(20:0.083297,21:0.089139):0.067194):0.006543):0.011062):0.005229):0.00803,((7:0.090648,(6:0.150383,8:0.133021):0.006503):0.01198,((36:0.062932,(38:0.066525,(37:0.076473,(35:0.039222,33:0.031429):0.00357):0.008228):0.005968):0.026714,((44:0.081521,(42:0.046822,43:0.059428):0.024607):0.004257,((39:0.046001,(40:0.029049,41:0.029533):0.003965):0.022397,((28:0.093611,29:0.050095):0.013432,(30:0.061026,(31:0.018601,32:0.018701):0.036144):0.004989):0.015808):0.001216):0.000872):0.002868):0.009567):0.010713):0.00234):0.1546885);
          tree tree.165000.208997.199794 = ((1:0.07628,2:0.065151):0.1546885,(((15:0.133631,(9:0.157087,10:0.077841):0.007403):0.005959,(11:0.0406,(12:0.092769,13:0.052284):0.000485):0.01453):0.029813,((4:0.05807,(3:0.054688,5:0.062757):0.008238):0.029441,(((26:0.083487,(24:0.064103,25:0.110063):0.002826):0.000775,((22:0.058663,23:0.116805):0.045375,(17:0.0898,((18:0.039267,19:0.043896):0.125808,(20:0.083297,21:0.089139):0.067194):0.006543):0.011062):0.003736):0.00803,((7:0.090648,(6:0.150383,8:0.133021):0.010132):0.01198,((44:0.084486,(42:0.046822,43:0.059428):0.024607):0.004257,((36:0.062932,(38:0.066525,(37:0.076473,(35:0.039222,33:0.031429):0.004674):0.008228):0.005968):0.026714,((39:0.046001,(40:0.029049,41:0.029533):0.003965):0.022397,((28:0.093611,29:0.050095):0.008576,(30:0.061026,(31:0.018601,32:0.018701):0.036144):0.004989):0.015808):0.001216):0.000872):0.002868):0.009567):0.010713):0.00234):0.1546885);
  ;
  
  
  end;
  
  </code></pre>
  <p>Why are these formats different and how can I make my file to look like the example one?
  Keep in mind the files are not presented in their entirety because I'm limited with the amount of characters.</p>
  <p>Edit: I will be providing my tree in this link <a href="https://drive.google.com/file/d/1lYmzW9htwaclC_yYs3fQom-Z3zbjk8wH/view?usp=sharing" rel="nofollow noreferrer">https://drive.google.com/file/d/1lYmzW9htwaclC_yYs3fQom-Z3zbjk8wH/view?usp=sharing</a></p>
  
Tags: <phylogenetics><phylogeny><file-formats>
Title: How can I convert my tree to the correct nexus format?
ThreadText: # How can I convert my tree to the correct nexus format?
  
  (Asked by: username_0 on 2023-10-10)
  
  I would like to use the program BayesTraitV4. I have my phylogenetic tree in NEXUS format but the program does not accept it. I checked the example data and while they are also in NEXUS format, they seemed different. I will provide a part of my data and the example data respectively.
  
  My tree:
  
  ```
  #NEXUS
  begin taxa;
      dimensions ntax=85;
      taxlabels
      LevantinaFC4779
      Assyriella_naegelei
      Ceu_LAG_2
      CeuMist2
      CeuMist1
      Ceu_PAN_2
      Ceu_PAN_1
      Ceu_PAN_3
      Ceu_PAN_4
      CcMath1
      CcNav1
      CcNav2
      Cc_Mal_1
      Cc_KalR2_2
      CcRod1
      CcRod2
      CcRod3
      CcRod4
      CcHr1
      CeST6_1
      CeST6_4
      CeST6_5
      CeAA7_1
      CeST6_3
      CeST6_2
      Cg_MelR7_1
      Cg_MelR3_1
      Cg_MelR6_2
      Cg_MelR7_2
      Cg_MelR6_1
      Cg_MelR7_3
      Cg_MelR5_1
      Cg_MelR4_2
      Cg_MelR1_1
      Cg_MelR2_1
      Cg_MelR4_1
      Cg_MelR7_4
      Cg_MelR5_2
      ChTM4_2
      ChTM5_1
      ChTM4_3
      ChTM4_1
      Ch_MEN_5
      Ch_MEN_13
      Ch_MEN_8
      Ch_LEV_3
      Ch_LEV_5
      Ch_LEV_4
      Ch_MEN_6
      Ch_MEN_10
      Ch_LEV_2
      Ch_MEN_4
      Ch_MEN_14
      Ch_LEV_1
      Ch_MEN_11
      Ch_MEN_3
      Ch_MEN_9
      Ci_MSP_3
      Ci_MSP_2
      Ci_MSP_1
      Ci_DIA_1
      Ci_DIA_2
      CiPLAN1
      CiPLAN3
      CiPLAN2
      Ci_MEN_1
      Ci_MEN_2
      Ci_MEN_12
      CpGravR6_1
      CpGravR3
      CpGravR4
      CpGio_2
      CpGravR5_2
      CpGravR2
      CpGravR7
      CpGio_1
      CpGio_3
      CpGravR1
      CpGravR6_2
      CpGravR5_1
      CpThe_1
      CpSka_1
      Cn_IG_2
      Cn_IG_3
      Cn_IG_1
  ;
  end;
  
  begin trees;
      tree TREE1 = [&R] ((LevantinaFC4779[&rate_range={7.888601174550756E-4,0.2727277039812744},height_95%_HPD={0.0,1.5711876244495215E-12},length_range={0.6843282088933,6.197383612374},height_median=6.004086117172847E-13,length_95%_HPD={1.080900382604,3.875114824373},height=6.614724410322848E-13,rate=0.049900260878735954,height_range={0.0,5.799805080641818E-12},rate_median=0.045084434131968686,length=2.411967820837161,length_median=2.3472043999879997,rate_95%_HPD={0.0108358382756707,0.10141567250363237}]:2.4119678208371664,Assyriella_naegelei[&rate_range={2.4004562386929353E-4,0.19480057878691465},height_95%_HPD={0.0,1.5711876244495215E-12},length_range={0.6843282088933,6.197383612374},height_median=6.004086117172847E-13,length_95%_HPD={1.080900382604,3.875114824373},height=6.614724410322848E-13,rate=0.03027613080757391,height_range={0.0,5.799805080641818E-
  
  ```
  
  Example tree:
  
  ```
  #NEXUS
  Begin trees;
      translate
          1   Opossum,
          2   Diprotodontian,
          3   Sloth,
          4   Armadillo,
          5   Anteater,
          6   Hedgehog,
          7   Mole,
          8   Shrew,
          9   Tenrecid,
          10  Golden_Mole,
          11  Sirenian,
          12  Hyrax,
          13  Elephant,
          15  Lo_Ear_Ele_shrew,
          17  Sciurid,
          18  Mouse,
          19  Rat,
          20  Hystricid,
          21  Caviomorph,
          22  Rabbit,
          23  Pika,
          24  Flying_Lemur,
          25  Tree_Shrew,
          26  Strepsirrhine,
          28  Phyllostomid,
          29  Free_tailed_bat,
          30  False_vampire_bat,
          31  Flying_Fox,
          32  Rousette_Fruitbat,
          33  Whale,
          35  Hippo,
          36  Llama,
          37  Ruminant,
          38  Pig,
          39  Horse,
          40  Rhino,
          41  Tapir,
          42  Cat,
          43  Caniform,
          44  Pangolin;
          tree tree.164000.208997.409491 = ((1:0.07628,2:0.065151):0.1546885,(((15:0.133631,(9:0.157087,10:0.077841):0.007403):0.005959,(11:0.0406,(12:0.092769,13:0.052284):0.001099):0.01453):0.029813,((4:0.05807,(3:0.054688,5:0.062757):0.008238):0.029441,(((26:0.083487,(24:0.064103,25:0.110063):0.003501):0.000775,((22:0.058663,23:0.116805):0.045375,(17:0.0898,((18:0.039267,19:0.043896):0.125808,(20:0.083297,21:0.089139):0.067194):0.006543):0.011062):0.005229):0.00803,((7:0.090648,(6:0.150383,8:0.133021):0.006503):0.01198,((36:0.062932,(38:0.066525,(37:0.076473,(35:0.039222,33:0.031429):0.00357):0.008228):0.005968):0.026714,((44:0.081521,(42:0.046822,43:0.059428):0.024607):0.004257,((39:0.046001,(40:0.029049,41:0.029533):0.003965):0.022397,((28:0.093611,29:0.050095):0.013432,(30:0.061026,(31:0.018601,32:0.018701):0.036144):0.004989):0.015808):0.001216):0.000872):0.002868):0.009567):0.010713):0.00234):0.1546885);
          tree tree.165000.208997.199794 = ((1:0.07628,2:0.065151):0.1546885,(((15:0.133631,(9:0.157087,10:0.077841):0.007403):0.005959,(11:0.0406,(12:0.092769,13:0.052284):0.000485):0.01453):0.029813,((4:0.05807,(3:0.054688,5:0.062757):0.008238):0.029441,(((26:0.083487,(24:0.064103,25:0.110063):0.002826):0.000775,((22:0.058663,23:0.116805):0.045375,(17:0.0898,((18:0.039267,19:0.043896):0.125808,(20:0.083297,21:0.089139):0.067194):0.006543):0.011062):0.003736):0.00803,((7:0.090648,(6:0.150383,8:0.133021):0.010132):0.01198,((44:0.084486,(42:0.046822,43:0.059428):0.024607):0.004257,((36:0.062932,(38:0.066525,(37:0.076473,(35:0.039222,33:0.031429):0.004674):0.008228):0.005968):0.026714,((39:0.046001,(40:0.029049,41:0.029533):0.003965):0.022397,((28:0.093611,29:0.050095):0.008576,(30:0.061026,(31:0.018601,32:0.018701):0.036144):0.004989):0.015808):0.001216):0.000872):0.002868):0.009567):0.010713):0.00234):0.1546885);
  ;
  
  end;
  
  ```
  
  Why are these formats different and how can I make my file to look like the example one?
  Keep in mind the files are not presented in their entirety because I'm limited with the amount of characters.
  
  Edit: I will be providing my tree in this link <https://drive.google.com/file/d/1lYmzW9htwaclC_yYs3fQom-Z3zbjk8wH/view?usp=sharing>
  
  **Tags:** phylogenetics, phylogeny, file-formats
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-10-10. Score: 2 | Accepted answer
  
  Okay ... this will probably work
  
  ```
  #NEXUS
  begin trees;
      tree TREE1 = [&R] ((LevantinaFC4779:2.411968,Assyriella_naegelei:2.411968):5.752052,((Cn_IG_1:0.126901,(Cn_IG_2:0.075971,Cn_IG_3:0.075971):0.05093):7.4805,(((CpThe_1:0.122189,CpSka_1:0.122189):2.663216,((CpGio_2:0.137489,(CpGravR6_1:0.087156,(CpGravR3:0.038234,CpGravR4:0.038234):0.048922):0.050334):0.257308,(CpGravR5_1:0.28159,((CpGravR7:0.099712,(CpGravR5_2:0.020255,CpGravR2:0.020255):0.079458):0.15617,(CpGravR6_2:0.109222,(CpGio_1:0.068711,(CpGio_3:0.049345,CpGravR1:0.049345):0.019367):0.040511):0.14666):0.025708):0.113207):2.390607):1.772627,(((Ci_MEN_12:0.072368,(Ci_MEN_1:0.022725,Ci_MEN_2:0.022725):0.049643):1.78894,((CiPLAN2:0.253487,(CiPLAN1:0.067509,CiPLAN3:0.067509):0.185978):0.386279,((Ci_MSP_3:0.061614,Ci_MSP_2:0.061614):0.231268,(Ci_MSP_1:0.113777,(Ci_DIA_1:0.047073,Ci_DIA_2:0.047073):0.066704):0.179105):0.346885):1.221542):1.580745,(((Ceu_LAG_2:1.580984,(CeuMist2:0.198982,CeuMist1:0.198982):1.382002):0.341226,((Ceu_PAN_2:0.046898,Ceu_PAN_1:0.046898):0.20368,(Ceu_PAN_3:0.018814,Ceu_PAN_4:0.018814):0.231764):1.671632):1.226475,((CcHr1:1.247104,((CcRod1:0.403751,(CcRod4:0.276104,(CcRod2:0.158977,CcRod3:0.158977):0.117127):0.127647):0.308704,((Cc_Mal_1:0.138232,Cc_KalR2_2:0.138232):0.395435,(CcMath1:0.338389,(CcNav1:0.091762,CcNav2:0.091762):0.246627):0.195278):0.178788):0.534649):1.609976,(((CeST6_5:0.056918,(CeST6_1:0.030107,CeST6_4:0.030107):0.026812):0.733078,((CeST6_2:0.143014,(CeAA7_1:0.097814,CeST6_3:0.097814):0.0452):0.349431,((Cg_MelR7_1:0.136715,(Cg_MelR3_1:0.088065,(Cg_MelR6_2:0.047987,(Cg_MelR7_2:0.019268,Cg_MelR6_1:0.019268):0.028719):0.040078):0.04865):0.074941,(Cg_MelR5_2:0.143401,(Cg_MelR7_3:0.119131,(Cg_MelR5_1:0.090065,((Cg_MelR4_1:0.020938,Cg_MelR7_4:0.020938):0.051613,(Cg_MelR4_2:0.052913,(Cg_MelR1_1:0.021387,Cg_MelR2_1:0.021387):0.031526):0.019639):0.017514):0.029066):0.02427):0.068255):0.280789):0.297551):0.793423,(((ChTM4_2:0.049871,ChTM5_1:0.049871):0.111934,(ChTM4_3:0.023134,ChTM4_1:0.023134):0.138672):0.228306,(Ch_MEN_9:0.174548,((Ch_MEN_11:0.021817,Ch_MEN_3:0.021817):0.10954,((Ch_MEN_8:0.057141,(Ch_MEN_5:0.022973,Ch_MEN_13:0.022973):0.034168):0.053065,((Ch_LEV_3:0.031056,Ch_LEV_5:0.031056):0.061225,((Ch_LEV_4:0.029359,(Ch_MEN_6:0.017456,Ch_MEN_10:0.017456):0.011904):0.034407,((Ch_LEV_2:0.017911,Ch_MEN_4:0.017911):0.040741,(Ch_MEN_14:0.03419,Ch_LEV_1:0.03419):0.024462):0.005114):0.028515):0.017925):0.021151):0.043191):0.215563):1.193307):1.27366):0.291605):0.293368):1.115978):3.04937):0.556619);
  end;
  
  ```
  
  Alternatively, I'm not sure about the root, just remove `[&R]` in the above.
  
  Finally there could be an issue that you haven't obtained the sample directly from the raw Beast output, instead you've summarised it. It might complain about that. Thus it might need all those trees from the raw Beast output. Thats not a format issue it's a data input issue. BayesTraits might be perform the calculation against the total MCMCMC sample minus the burn-in.
  
  ---
  
  from comments
  
  Read it into Rs `ape::read.nexus()` and then write via `phytools::writeNexus()`. This should produce your translate table. Biopython recognises this format but doesn't write to it.
  
  The closest Biopython can achieve is a taxablock here
  
  ```
  #NEXUS
  Begin Taxa;
   Dimensions NTax=85;
   TaxLabels LevantinaFC4779 Assyriella_naegelei Cn_IG_1 Cn_IG_2 Cn_IG_3 CpThe_1 CpSka_1 CpGio_2 CpGravR6_1 CpGravR3 CpGravR4 CpGravR5_1 CpGravR7 CpGravR5_2 CpGravR2 CpGravR6_2 CpGio_1 CpGio_3 CpGravR1 Ci_MEN_12 Ci_MEN_1 Ci_MEN_2 CiPLAN2 CiPLAN1 CiPLAN3 Ci_MSP_3 Ci_MSP_2 Ci_MSP_1 Ci_DIA_1 Ci_DIA_2 Ceu_LAG_2 CeuMist2 CeuMist1 Ceu_PAN_2 Ceu_PAN_1 Ceu_PAN_3 Ceu_PAN_4 CcHr1 CcRod1 CcRod4 CcRod2 CcRod3 Cc_Mal_1 Cc_KalR2_2 CcMath1 CcNav1 CcNav2 CeST6_5 CeST6_1 CeST6_4 CeST6_2 CeAA7_1 CeST6_3 Cg_MelR7_1 Cg_MelR3_1 Cg_MelR6_2 Cg_MelR7_2 Cg_MelR6_1 Cg_MelR5_2 Cg_MelR7_3 Cg_MelR5_1 Cg_MelR4_1 Cg_MelR7_4 Cg_MelR4_2 Cg_MelR1_1 Cg_MelR2_1 ChTM4_2 ChTM5_1 ChTM4_3 ChTM4_1 Ch_MEN_9 Ch_MEN_11 Ch_MEN_3 Ch_MEN_8 Ch_MEN_5 Ch_MEN_13 Ch_LEV_3 Ch_LEV_5 Ch_LEV_4 Ch_MEN_6 Ch_MEN_10 Ch_LEV_2 Ch_MEN_4 Ch_MEN_14 Ch_LEV_1;
  End;
  Begin Trees;
   Tree tree1=((LevantinaFC4779:2.41197,Assyriella_naegelei:2.41197):5.75205,((Cn_IG_1:0.12690,(Cn_IG_2:0.07597,Cn_IG_3:0.07597):0.05093):7.48050,(((CpThe_1:0.12219,CpSka_1:0.12219):2.66322,((CpGio_2:0.13749,(CpGravR6_1:0.08716,(CpGravR3:0.03823,CpGravR4:0.03823):0.04892):0.05033):0.25731,(CpGravR5_1:0.28159,((CpGravR7:0.09971,(CpGravR5_2:0.02025,CpGravR2:0.02025):0.07946):0.15617,(CpGravR6_2:0.10922,(CpGio_1:0.06871,(CpGio_3:0.04934,CpGravR1:0.04934):0.01937):0.04051):0.14666):0.02571):0.11321):2.39061):1.77263,(((Ci_MEN_12:0.07237,(Ci_MEN_1:0.02272,Ci_MEN_2:0.02272):0.04964):1.78894,((CiPLAN2:0.25349,(CiPLAN1:0.06751,CiPLAN3:0.06751):0.18598):0.38628,((Ci_MSP_3:0.06161,Ci_MSP_2:0.06161):0.23127,(Ci_MSP_1:0.11378,(Ci_DIA_1:0.04707,Ci_DIA_2:0.04707):0.06670):0.17910):0.34688):1.22154):1.58075,(((Ceu_LAG_2:1.58098,(CeuMist2:0.19898,CeuMist1:0.19898):1.38200):0.34123,((Ceu_PAN_2:0.04690,Ceu_PAN_1:0.04690):0.20368,(Ceu_PAN_3:0.01881,Ceu_PAN_4:0.01881):0.23176):1.67163):1.22647,((CcHr1:1.24710,((CcRod1:0.40375,(CcRod4:0.27610,(CcRod2:0.15898,CcRod3:0.15898):0.11713):0.12765):0.30870,((Cc_Mal_1:0.13823,Cc_KalR2_2:0.13823):0.39543,(CcMath1:0.33839,(CcNav1:0.09176,CcNav2:0.09176):0.24663):0.19528):0.17879):0.53465):1.60998,(((CeST6_5:0.05692,(CeST6_1:0.03011,CeST6_4:0.03011):0.02681):0.73308,((CeST6_2:0.14301,(CeAA7_1:0.09781,CeST6_3:0.09781):0.04520):0.34943,((Cg_MelR7_1:0.13672,(Cg_MelR3_1:0.08807,(Cg_MelR6_2:0.04799,(Cg_MelR7_2:0.01927,Cg_MelR6_1:0.01927):0.02872):0.04008):0.04865):0.07494,(Cg_MelR5_2:0.14340,(Cg_MelR7_3:0.11913,(Cg_MelR5_1:0.09007,((Cg_MelR4_1:0.02094,Cg_MelR7_4:0.02094):0.05161,(Cg_MelR4_2:0.05291,(Cg_MelR1_1:0.02139,Cg_MelR2_1:0.02139):0.03153):0.01964):0.01751):0.02907):0.02427):0.06825):0.28079):0.29755):0.79342,(((ChTM4_2:0.04987,ChTM5_1:0.04987):0.11193,(ChTM4_3:0.02313,ChTM4_1:0.02313):0.13867):0.22831,(Ch_MEN_9:0.17455,((Ch_MEN_11:0.02182,Ch_MEN_3:0.02182):0.10954,((Ch_MEN_8:0.05714,(Ch_MEN_5:0.02297,Ch_MEN_13:0.02297):0.03417):0.05307,((Ch_LEV_3:0.03106,Ch_LEV_5:0.03106):0.06123,((Ch_LEV_4:0.02936,(Ch_MEN_6:0.01746,Ch_MEN_10:0.01746):0.01190):0.03441,((Ch_LEV_2:0.01791,Ch_MEN_4:0.01791):0.04074,(Ch_MEN_14:0.03419,Ch_LEV_1:0.03419):0.02446):0.00511):0.02851):0.01792):0.02115):0.04319):0.21556):1.19331):
  1.27366):0.29161):0.29337):1.11598):3.04937):0.55662):0.00000;
  End;
  
  ```
  
  The solution could be coded from the taxa block if the above doesn't work, but easier to use **R** `ape` and `phytools`
  
  > **Comments:**
  > **username_0**: I tried using this tree you provided as input and got this message:  Err: Does have a translate line.  
  
  ---
  
  