Hi Peter,

You can start with the aligned-sequence-data file, set them in *.nex format, and open the file by choosing Import Data>Sequences [click Text file of multiple sequences (Nexus Format)]. Go to Raw data>Process Seqs and select Find Haplotypes, Seq by Nuc and Color Sequence. Then, several working sheets will appear, go to the sheet with the name PN, in PN, input the information for "Pop" with numbers (1= Population A, 2- Populations B and etc.) and insert another column for the "Locality" and similar to "Pop", add in the locality represents by numbers. Lastly, copy the data in PN start from row number three until the end of the dataset and paste it into a new 'text document.txt'. Delete "Sample" "Pop" and "Locality", save the file, remove the ".txt" extension, and you are ready for STRUCTURE.

Hope this help.

Cheers, HongChang

Hi, thanks for the reply. But I need the GeneAlex (http://biology-assets.anu.edu.au/GenAlEx/Welcome.html) format, not Structure. If it's not the same. And BTW for STRUCTURE I'd use the program PGDSpider which can convert directly.

Hi Peter, might be a bit late, but you can import nexus files into GenAlEx. Once it's in (Use GenAlEx > Import Data and choose your data file type and locate) I needed to find and replace the base letters with numbers in the SQ sheet - and check that it saw my populations. The tutorial #1 on http://biology-assets.anu.edu.au/GenAlEx/Tutorials.html is useful for showing what your file should look like before you run analyses. 

Thanks a lot, that's helpful

Can any one help how to make haplotypes from MLVA allele profiles using Genalex or any other software?

Hi everyone, how can one enter alleles for an indel in GenAIEx e.g. GAT>_?

hi, I have an SSR dataset and would like to bring them from genalex to poppr but I can’t. can you help me with some sample files?

thanks