text: user14041: I have Arlequin output files (*.arp) from fastSimcoal2 that I'm trying to convert to genepop files (to read into adegenet). The Arlequin files are using the "DNA" marker (50 bp long), and each includes ~2,500 samples.
  When trying to use the program PGDspider to convert these (either the GUI or the CLI; v2.1.1.5), things proceed smoothly until the 1,000th allele is reached, where the program generates an error:
  INFO  07-03 11:18:10,630 (GenepopWriter.java:parseAlignedSampleData:596)  -Allele "TGGCATCAGCTTCTTCTAAGCAGGCCCGCTTTGTCTAGCGACAGATCTCG" converted to "999"
  INFO  07-03 11:18:10,630 (GenepopWriter.java:parseAlignedSampleData:596)  -Allele "ATCTTGTGGTCATGGAGCACCCAGAGCCAAACTCCTAAAGAAGACCCCGC" converted to "1000"
  ERROR 07-03 11:18:10,630 (GenepopWriter.java:parseAlignedSampleData:611)  -data "1000" in ind "2_375" (population: Sample 2) is too long!!!
  INFO  07-03 11:18:10,631 (GenepopWriter.java:parseAlignedSampleData:618)  -In GENEPOP, alleles cannot be coded with more than 3 digits.
  
  Is there a way around this error? I've processed RADseq data with many 1,000s of alleles using adegenet before, so I know these types of files can be written into genpop--I just don't know how to specify this to PGDspider. There's a field in the .spid file that I might be able to use to fix this (see below), but I don't know what to populate that field with, and there aren't any suggestions from the (limited) documentation.
  # Specify the locus/locus combination you want to write to the GENEPOP file:
  GENEPOP_WRITER_LOCUS_COMBINATION_QUESTION=
  
  Alternatively, if there are suggestions for running this conversion without using PGDspider, I'm all ears.
  Thanks for your help!
  
  user14041: Ultimately, I achieved this using the R package strataG. The steps taken (in R) are shown below.
  arp.object <- arlequinRead(arp.path)
  gtype.object <- arp2gtypes(arp.object)
  genind.object <- gtypes2genind(gtype.object)
  
  I found that fastSimcoal2 shows an odd behavior when simulating DNA markers, in which sequences are concatenated together (regardless of marker blocks specified; relevant post here). Running the fastSimcoal2 simulations from strataG addressed this bug (and is more straightforward/reproducible, anyways).
  
original_text: 14041: <p>I have <a href="http://cmpg.unibe.ch/software/arlequin35/" rel="nofollow noreferrer">Arlequin</a> output files (*.arp) from <a href="http://cmpg.unibe.ch/software/fastsimcoal27/" rel="nofollow noreferrer">fastSimcoal2</a> that I'm trying to convert to genepop files (to read into <a href="https://cran.r-project.org/web/packages/adegenet/index.html" rel="nofollow noreferrer">adegenet</a>). The Arlequin files are using the &quot;DNA&quot; marker (50 bp long), and each includes ~2,500 samples.</p>
  <p>When trying to use the program <a href="http://www.cmpg.unibe.ch/software/PGDSpider/#Download_and_Installation_Instructions" rel="nofollow noreferrer">PGDspider</a> to convert these (either the GUI or the CLI; v2.1.1.5), things proceed smoothly until the 1,000th allele is reached, where the program generates an error:</p>
  <pre><code>INFO  07-03 11:18:10,630 (GenepopWriter.java:parseAlignedSampleData:596)  -Allele &quot;TGGCATCAGCTTCTTCTAAGCAGGCCCGCTTTGTCTAGCGACAGATCTCG&quot; converted to &quot;999&quot;
  INFO  07-03 11:18:10,630 (GenepopWriter.java:parseAlignedSampleData:596)  -Allele &quot;ATCTTGTGGTCATGGAGCACCCAGAGCCAAACTCCTAAAGAAGACCCCGC&quot; converted to &quot;1000&quot;
  ERROR 07-03 11:18:10,630 (GenepopWriter.java:parseAlignedSampleData:611)  -data &quot;1000&quot; in ind &quot;2_375&quot; (population: Sample 2) is too long!!!
  INFO  07-03 11:18:10,631 (GenepopWriter.java:parseAlignedSampleData:618)  -In GENEPOP, alleles cannot be coded with more than 3 digits.
  </code></pre>
  <p>Is there a way around this error? I've processed RADseq data with many 1,000s of alleles using adegenet before, so I know these types of files can be written into genpop--I just don't know how to specify this to PGDspider. There's a field in the .spid file that I might be able to use to fix this (see below), but I don't know what to populate that field with, and there aren't any suggestions from the (limited) documentation.</p>
  <pre><code># Specify the locus/locus combination you want to write to the GENEPOP file:
  GENEPOP_WRITER_LOCUS_COMBINATION_QUESTION=
  </code></pre>
  <p>Alternatively, if there are suggestions for running this conversion without using PGDspider, I'm all ears.</p>
  <p>Thanks for your help!</p>
   14041: <p>Ultimately, I achieved this using the R package <a href="https://github.com/EricArcher/strataG" rel="nofollow noreferrer">strataG</a>. The steps taken (in R) are shown below.</p>
  <pre><code>arp.object &lt;- arlequinRead(arp.path)
  gtype.object &lt;- arp2gtypes(arp.object)
  genind.object &lt;- gtypes2genind(gtype.object)
  </code></pre>
  <p>I found that fastSimcoal2 shows an odd behavior when simulating DNA markers, in which sequences are concatenated together (regardless of marker blocks specified; relevant post <a href="https://groups.google.com/g/fastsimcoal/c/cVT2jU7sqxA" rel="nofollow noreferrer">here</a>). Running the fastSimcoal2 simulations from strataG addressed this bug (and is more straightforward/reproducible, anyways).</p>
  