Body: <p>I'm trying to create a map in <a href="http://popart.otago.ac.nz/index.shtml" rel="nofollow noreferrer">PopArt</a> that allows me to visualise the distribution of several species. These are my Traits (=species) and GeoTags blocks:</p>
  
  <pre><code>BEGIN TRAITS;
      Dimensions NTRAITS=9;
      Format labels=no missing=? separator=Comma;
      TraitLabels SNE Lsp A B C D 3n 4n Lep;
  Matrix
  SNE1 1,0,0,0,0,0,0,0,0
  SNE2 1,0,0,0,0,0,0,0,0
  SNE3 1,0,0,0,0,0,0,0,0
  SNE4 1,0,0,0,0,0,0,0,0
  SNE5 1,0,0,0,0,0,0,0,0
  SNE6 1,0,0,0,0,0,0,0,0
  PUR_4n 0,0,0,0,0,0,0,1,0
  GRA 0,1,0,0,0,0,0,0,0
  OJE 0,1,0,0,0,0,0,0,0
  ESC 0,0,0,0,0,0,0,0,1
  LNM 0,0,0,0,0,0,0,0,1
  PIN 0,0,0,0,0,0,0,0,1
  URD 0,0,0,0,0,0,0,0,1
  VIS 0,0,0,0,0,0,0,0,1
  LYE 0,0,0,0,0,0,0,0,1
  BEN_A 0,0,1,0,0,0,0,0,0
  ALJ1_A 0,0,1,0,0,0,0,0,0
  ALJ2_A 0,0,1,0,0,0,0,0,0
  ESP2_B 0,0,0,1,0,0,0,0,0
  ESP3_B 0,0,0,1,0,0,0,0,0
  ALC_C 0,0,0,0,1,0,0,0,0
  AVA1_3n 0,0,0,0,0,0,1,0,0
  AVA2_3n 0,0,0,0,0,0,1,0,0
  PER_3n 0,0,0,0,0,0,1,0,0
  TRI_3n 0,0,0,0,0,0,1,0,0
  VDI_3n 0,0,0,0,0,0,1,0,0
  VIL_3n 0,0,0,0,0,0,1,0,0
  CVE1_4n 0,0,0,0,0,0,0,1,0
  CVE2_4n 0,0,0,0,0,0,0,1,0
  LNA1_4n 0,0,0,0,0,0,0,1,0
  LNA2_4n 0,0,0,0,0,0,0,1,0
  PRA1_4n 0,0,0,0,0,0,0,1,0
  PRA2_4n 0,0,0,0,0,0,0,1,0
  VEN1_4n 0,0,0,0,0,0,0,1,0
  VEN2_4n 0,0,0,0,0,0,0,1,0
  ZAR_4n 0,0,0,0,0,0,0,1,0
  SFI1 0,0,0,0,0,0,0,0,1
  SFI2 0,0,0,0,0,0,0,0,1
  SIB 0,0,0,0,0,0,0,0,1
  TIS1_D 0,0,0,0,0,1,0,0,0
  TIS2_D 0,0,0,0,0,1,0,0,0
  TIS3_D 0,0,0,0,0,1,0,0,0
  TIS4_D 0,0,0,0,0,1,0,0,0
  TVI_D 0,0,0,0,0,1,0,0,0
  PVRFAS0001 1,0,0,0,0,0,0,0,0
  PVRFAS0002 1,0,0,0,0,0,0,0,0
  PVRFAS0024 1,0,0,0,0,0,0,0,0
  PVRFAS0025 1,0,0,0,0,0,0,0,0
  PVRFAS0027 1,0,0,0,0,0,0,0,0
  PVRFAS0028 1,0,0,0,0,0,0,0,0
  ;
  END;
  Begin GeoTags;
      Dimensions NClusts=29;
      Format labels=no separator=Spaces;
      [ClustLatitude 37.15 37.77 37.13 39.37 37.11 40.60 40.59 37.04 40.61 38.71 36.70 43.48 40.18 40.24 40.57 40.26 37.10 37.86 38.52 36.56 40.23 38.01 39.58 38.75 40.54 40.55 38.70 40.04 40.69;
      ClustLongitude -3.70 -3.02 -3.52 -3.72 -3.03 -4.33 -4.33 -3.43 -2.44 0.05 -5.35 3.55 -6.55 -2.06 -4.16 0.26 -3.26 -1.56 -3.56 -4.86 -2.07 -2.87 -3.87 0.18 -4.18 -4.19 -0.49 -7.49 -2.59;]
  Matrix
  SNE1 37.044888 -3.135564
  SNE2 37.044888 -3.135564
  SNE3 37.044888 -3.135564
  SNE4 37.044888 -3.135564
  SNE5 37.044888 -3.135564
  SNE6 37.044888 -3.135564
  PUR_4n 37.133158 -3.524806
  GRA 36.708272 -5.348794
  OJE 36.562847 -4.853522
  ESC 40.5659132 -4.2236186
  LNM 40.609845 -4.344144
  PIN 38.752157 0.180615
  URD 39.370381 -3.720659
  VIS 38.520059 -3.564201
  LYE 39.580131 -3.870267
  BEN_A 38.712603 0.052372
  ALJ1_A 38.704010 -0.490801
  ALJ2_A 38.704010 -0.490801
  ESP2_B 37.865615 -1.569499
  ESP3_B 37.865615 -1.569499
  ALC_C 40.264366 0.267744
  AVA1_3n 43.490194 3.563363
  AVA2_3n 43.490194 3.563363
  PER_3n 40.610461 -2.447806
  TRI_3n 40.697087 -2.595488
  VDI_3n 40.244599 -2.067766
  VIL_3n 40.231843 -2.078962
  CVE1_4n 40.559003 -4.199853
  CVE2_4n 40.559003 -4.199853
  LNA1_4n 40.597289 -4.330246
  LNA2_4n 40.597289 -4.330246
  PRA1_4n 37.113314 -3.035071
  PRA2_4n 37.113314 -3.035071
  VEN1_4n 37.155124 -3.703330
  VEN2_4n 37.155124 -3.703330
  ZAR_4n 40.547662 -4.184395
  SFI1 40.042132 -7.498515
  SFI2 40.042132 -7.498515
  SIB 40.182598 -6.551259
  TIS1_D 37.771593 -3.023286
  TIS2_D 37.771593 -3.023286
  TIS3_D 37.771593 -3.023286
  TIS4_D 37.771593 -3.023286
  TVI_D 38.0140003 -2.8751617
  PVRFAS0001 37.100000 -3.260000
  PVRFAS0002 37.100000 -3.260000
  PVRFAS0024 37.100000 -3.260000
  PVRFAS0025 37.100000 -3.260000
  PVRFAS0027 37.100000 -3.260000
  PVRFAS0028 37.100000 -3.260000
  ;
  End;
  </code></pre>
  
  <ul>
  <li>If I upload my Nexus file like this, the program throws an error saying "Too many rows in GeoTags block." However, I have 50 samples in both Traits and GeoTags. The same happens if I uncomment (in Nexus format, comments are in brackets) the ClustLatitude and ClustLongitude files. </li>
  <li>If I set the "labels" flag on "yes", it takes the traits as the geographical locations and tries to find locations in the world starting with the trait names. </li>
  <li>If I comment the "GeoTags" block, PopArt correctly outputs a network.</li>
  </ul>
  
  <p>What am I missing? Does somebody have a Nexus example where the traits do not correspond to geographical location of the samples?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-19T07:10:30.183Z
Comments.Text: I don't know this format but you seem to have two BEGIN and two ENDs. To me it looks like you have two datasets in one. Also one is in caps and the other is not. Are you sure that the file is in the right format? Did you check it (if there is any tool to do that) ?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-19T09:24:32.217Z
Comments.Text: This program uses a custom version of the Nexus format. Here is the manual: http://popart.otago.ac.nz/doc/popart.pdf and it uses exactly the "begin" and "end" blocks I'm using - weird format, I know, but I'm trying to stick as much as possible to the example given...
Comments.UserDisplayName: LinuxBlanket
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-19T09:26:31.780Z
Comments.Text: @Llopis Additional info [here](https://besjournals.onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1111%2F2041-210X.12410&file=mee312410-sup-0001-Supinfo.pdf) (Supplementary data of the PopArt paper) and [here](http://popart.otago.ac.nz/examplenex.shtml) (Nexus example in the PopArt site)
Comments.UserDisplayName: LinuxBlanket
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-19T09:32:16.413Z
Comments.Text: In the pdf you link in the first comment the traits data is formatted different (see the corresponding section of "Traits Tables"). Are you sure you should provide all these data in a single file? The error seems to imply that when an END is found it should be the end of the file or something alike.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-19T09:36:36.160Z
Comments.Text: Ah you mean the indent? That's a copy-paste error, I'll edit that. In the original file I indented the block between "BEGIN TRAITS" and "Matrix". Note that if I comment the GeoTags block, a network is produced correctly. The manual notes: " I've separated the individual blocks with text describing the important points, but they should all be included in a single text file, as shown in here."
Comments.UserDisplayName: LinuxBlanket
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-19T11:04:57.063Z
Comments.Text: No, I mean that the section "traits Tables" describe a different format (coma separated values I think) than the one you have, but trait information is described in two formats.
Comments.UserDisplayName: llrs
Tags: <networks><haplotypes>
Title: How to format the Nexus file to create geographical maps with haplotypes in PopArt?
ThreadText: # How to format the Nexus file to create geographical maps with haplotypes in PopArt?
  
  (Asked by: username_0 on 2018-09-18)
  
  I'm trying to create a map in [PopArt](http://popart.otago.ac.nz/index.shtml) that allows me to visualise the distribution of several species. These are my Traits (=species) and GeoTags blocks:
  
  ```
  BEGIN TRAITS;
      Dimensions NTRAITS=9;
      Format labels=no missing=? separator=Comma;
      TraitLabels SNE Lsp A B C D 3n 4n Lep;
  Matrix
  SNE1 1,0,0,0,0,0,0,0,0
  SNE2 1,0,0,0,0,0,0,0,0
  SNE3 1,0,0,0,0,0,0,0,0
  SNE4 1,0,0,0,0,0,0,0,0
  SNE5 1,0,0,0,0,0,0,0,0
  SNE6 1,0,0,0,0,0,0,0,0
  PUR_4n 0,0,0,0,0,0,0,1,0
  GRA 0,1,0,0,0,0,0,0,0
  OJE 0,1,0,0,0,0,0,0,0
  ESC 0,0,0,0,0,0,0,0,1
  LNM 0,0,0,0,0,0,0,0,1
  PIN 0,0,0,0,0,0,0,0,1
  URD 0,0,0,0,0,0,0,0,1
  VIS 0,0,0,0,0,0,0,0,1
  LYE 0,0,0,0,0,0,0,0,1
  BEN_A 0,0,1,0,0,0,0,0,0
  ALJ1_A 0,0,1,0,0,0,0,0,0
  ALJ2_A 0,0,1,0,0,0,0,0,0
  ESP2_B 0,0,0,1,0,0,0,0,0
  ESP3_B 0,0,0,1,0,0,0,0,0
  ALC_C 0,0,0,0,1,0,0,0,0
  AVA1_3n 0,0,0,0,0,0,1,0,0
  AVA2_3n 0,0,0,0,0,0,1,0,0
  PER_3n 0,0,0,0,0,0,1,0,0
  TRI_3n 0,0,0,0,0,0,1,0,0
  VDI_3n 0,0,0,0,0,0,1,0,0
  VIL_3n 0,0,0,0,0,0,1,0,0
  CVE1_4n 0,0,0,0,0,0,0,1,0
  CVE2_4n 0,0,0,0,0,0,0,1,0
  LNA1_4n 0,0,0,0,0,0,0,1,0
  LNA2_4n 0,0,0,0,0,0,0,1,0
  PRA1_4n 0,0,0,0,0,0,0,1,0
  PRA2_4n 0,0,0,0,0,0,0,1,0
  VEN1_4n 0,0,0,0,0,0,0,1,0
  VEN2_4n 0,0,0,0,0,0,0,1,0
  ZAR_4n 0,0,0,0,0,0,0,1,0
  SFI1 0,0,0,0,0,0,0,0,1
  SFI2 0,0,0,0,0,0,0,0,1
  SIB 0,0,0,0,0,0,0,0,1
  TIS1_D 0,0,0,0,0,1,0,0,0
  TIS2_D 0,0,0,0,0,1,0,0,0
  TIS3_D 0,0,0,0,0,1,0,0,0
  TIS4_D 0,0,0,0,0,1,0,0,0
  TVI_D 0,0,0,0,0,1,0,0,0
  PVRFAS0001 1,0,0,0,0,0,0,0,0
  PVRFAS0002 1,0,0,0,0,0,0,0,0
  PVRFAS0024 1,0,0,0,0,0,0,0,0
  PVRFAS0025 1,0,0,0,0,0,0,0,0
  PVRFAS0027 1,0,0,0,0,0,0,0,0
  PVRFAS0028 1,0,0,0,0,0,0,0,0
  ;
  END;
  Begin GeoTags;
      Dimensions NClusts=29;
      Format labels=no separator=Spaces;
      [ClustLatitude 37.15 37.77 37.13 39.37 37.11 40.60 40.59 37.04 40.61 38.71 36.70 43.48 40.18 40.24 40.57 40.26 37.10 37.86 38.52 36.56 40.23 38.01 39.58 38.75 40.54 40.55 38.70 40.04 40.69;
      ClustLongitude -3.70 -3.02 -3.52 -3.72 -3.03 -4.33 -4.33 -3.43 -2.44 0.05 -5.35 3.55 -6.55 -2.06 -4.16 0.26 -3.26 -1.56 -3.56 -4.86 -2.07 -2.87 -3.87 0.18 -4.18 -4.19 -0.49 -7.49 -2.59;]
  Matrix
  SNE1 37.044888 -3.135564
  SNE2 37.044888 -3.135564
  SNE3 37.044888 -3.135564
  SNE4 37.044888 -3.135564
  SNE5 37.044888 -3.135564
  SNE6 37.044888 -3.135564
  PUR_4n 37.133158 -3.524806
  GRA 36.708272 -5.348794
  OJE 36.562847 -4.853522
  ESC 40.5659132 -4.2236186
  LNM 40.609845 -4.344144
  PIN 38.752157 0.180615
  URD 39.370381 -3.720659
  VIS 38.520059 -3.564201
  LYE 39.580131 -3.870267
  BEN_A 38.712603 0.052372
  ALJ1_A 38.704010 -0.490801
  ALJ2_A 38.704010 -0.490801
  ESP2_B 37.865615 -1.569499
  ESP3_B 37.865615 -1.569499
  ALC_C 40.264366 0.267744
  AVA1_3n 43.490194 3.563363
  AVA2_3n 43.490194 3.563363
  PER_3n 40.610461 -2.447806
  TRI_3n 40.697087 -2.595488
  VDI_3n 40.244599 -2.067766
  VIL_3n 40.231843 -2.078962
  CVE1_4n 40.559003 -4.199853
  CVE2_4n 40.559003 -4.199853
  LNA1_4n 40.597289 -4.330246
  LNA2_4n 40.597289 -4.330246
  PRA1_4n 37.113314 -3.035071
  PRA2_4n 37.113314 -3.035071
  VEN1_4n 37.155124 -3.703330
  VEN2_4n 37.155124 -3.703330
  ZAR_4n 40.547662 -4.184395
  SFI1 40.042132 -7.498515
  SFI2 40.042132 -7.498515
  SIB 40.182598 -6.551259
  TIS1_D 37.771593 -3.023286
  TIS2_D 37.771593 -3.023286
  TIS3_D 37.771593 -3.023286
  TIS4_D 37.771593 -3.023286
  TVI_D 38.0140003 -2.8751617
  PVRFAS0001 37.100000 -3.260000
  PVRFAS0002 37.100000 -3.260000
  PVRFAS0024 37.100000 -3.260000
  PVRFAS0025 37.100000 -3.260000
  PVRFAS0027 37.100000 -3.260000
  PVRFAS0028 37.100000 -3.260000
  ;
  End;
  
  ```
  
  * If I upload my Nexus file like this, the program throws an error saying "Too many rows in GeoTags block." However, I have 50 samples in both Traits and GeoTags. The same happens if I uncomment (in Nexus format, comments are in brackets) the ClustLatitude and ClustLongitude files.
  * If I set the "labels" flag on "yes", it takes the traits as the geographical locations and tries to find locations in the world starting with the trait names.
  * If I comment the "GeoTags" block, PopArt correctly outputs a network.
  
  What am I missing? Does somebody have a Nexus example where the traits do not correspond to geographical location of the samples?
  
  **Tags:** networks, haplotypes
  
  > **Comments:**
  > **username_1**: I don't know this format but you seem to have two BEGIN and two ENDs. To me it looks like you have two datasets in one. Also one is in caps and the other is not. Are you sure that the file is in the right format? Did you check it (if there is any tool to do that) ?  
  > **username_0**: This program uses a custom version of the Nexus format. Here is the manual: http://popart.otago.ac.nz/doc/popart.pdf and it uses exactly the "begin" and "end" blocks I'm using - weird format, I know, but I'm trying to stick as much as possible to the example given...  
  > **username_0**: @Llopis Additional info [here](https://besjournals.onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1111%2F2041-210X.12410&file=mee312410-sup-0001-Supinfo.pdf) (Supplementary data of the PopArt paper) and [here](http://popart.otago.ac.nz/examplenex.shtml) (Nexus example in the PopArt site)  
  > **username_1**: In the pdf you link in the first comment the traits data is formatted different (see the corresponding section of "Traits Tables"). Are you sure you should provide all these data in a single file? The error seems to imply that when an END is found it should be the end of the file or something alike.  
  > **username_0**: Ah you mean the indent? That's a copy-paste error, I'll edit that. In the original file I indented the block between "BEGIN TRAITS" and "Matrix". Note that if I comment the GeoTags block, a network is produced correctly. The manual notes: " I've separated the individual blocks with text describing the important points, but they should all be included in a single text file, as shown in here."  
  > **username_1**: No, I mean that the section "traits Tables" describe a different format (coma separated values I think) than the one you have, but trait information is described in two formats.  
  
  ---
  
  ## 0 answers
  
  