I was advised to use Arlequin to do some calculation such as AMOVA. After figuring out I couldn't launch it on OSX, I started it on Windows but now I just don't know how to put my data in. It is a CSV file separated by tabs,( first line giving allele, first row sample ID) and the data is of binary values (dominant marker from AFLP).
Have you found an answer? For microsatellite data, I use Genalex to convert it to Genepop version. Then I use Genepop online version (http://genepop.curtin.edu.au/genepop_op7.html) to convert the data into Arlequin format. And this file works.
Genalex itself also converts it to Arlequin. But Arlequin has never recognized these converted files that I tried so far. I haven't discovered the reason yet.
By the way, Genalex is an easy program to use. It has macros working with Excel. (http://biology.anu.edu.au/GenAlEx/Welcome.html)
I am not sure about AFLP data but there should be a way with Genalex.
Have you found an answer? For microsatellite data, I use Genalex to convert it to Genepop version. Then I use Genepop online version (http://genepop.curtin.edu.au/genepop_op7.html) to convert the data into Arlequin format. And this file works.
Genalex itself also converts it to Arlequin. But Arlequin has never recognized these converted files that I tried so far. I haven't discovered the reason yet.
By the way, Genalex is an easy program to use. It has macros working with Excel. (http://biology.anu.edu.au/GenAlEx/Welcome.html)
I am not sure about AFLP data but there should be a way with Genalex.
I tried genalex… not so east to use… double pain (windows+excel) … I imported data in using the R export function… unfortunately genalex format has changed from on version to another… I had someone from my institution was mastering it …
so export to arlequin failed and results were just… well …
there is an Arlequin of OSX http://darwin.eeb.uconn.edu/Arlequin/index.html
But I have never tried it myself
Try pgdSpider for changing formats. It works for everything I tried
You can download Convert131 software which contains example file of input data. It can convert the file prepared (I did in excel format) in various format as I did to convert in arlquin format.
@Rajeev Kawatra: could you, please, provide the link of Convert131 program.
Leocadio Blanco-Bercial, did you try to convert txt files to arlquin format with pgdSpider ?
Yes - they are all "txt-like" files, really (but the genalex, that is a excel-like). The only think that changes is the internal structure.
But, if you have a genepop file, moving it into arlequin is easy both with PGD and genales.
Hi @fariba…
Maybe you should start a new topic for your question… Then… Don't forget to tell what is your actual format…
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