Hi all, 

I have [Arlequin][1] output files (*.arp) from [fastSimcoal2][2] that I'm trying to convert to genpop files (to read into [adegenet][3]). The Arlequin files are using the "DNA" marker (50 bp long), and each includes ~2,500 samples. 

When I try to use the program [PGDspider][4] to convert these files (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? I've processed RADseq data with many 1,000s of alleles using adegenet before, so I know these types of files can be written to 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.
```
# Specify the locus/locus combination you want to write to the GENEPOP file:
GENEPOP_WRITER_LOCUS_COMBINATION_QUESTION=
```

Alternatively, if there are other suggestions for performing this conversion without using PGDspider, I'm all ears. 

Thanks for your help!


  [1]: http://cmpg.unibe.ch/software/arlequin35/
  [2]: http://cmpg.unibe.ch/software/fastsimcoal27/
  [3]: https://cran.r-project.org/web/packages/adegenet/index.html
  [4]: http://www.cmpg.unibe.ch/software/PGDSpider/#Download_and_Installation_Instructions
Answer: I've been able to do this using the R package [strataG][1] (no longer on CRAN, but can be obtained on GitHub). Specifically, the steps are:

 1. Read in .arp file, e.g. arpObject <- arlequinRead(file.arp)
 2. Convert  arlequin object to gtype object (arp2gtypes function)
 3. Convert gtype object to genind object (gtypes2genind function)

  [1]: https://github.com/EricArcher/strataG