I am not experienced in Arlequin, just used it a bunch of times. However, on several papers never saw them mentioning MacClade.

I recommend you to check out the manual of the software which is much more detailed than that step by step manual. There you have info on how to calculate what you want. It will take you a while, but you can do so much things in Arlequin, it will worth it...

Check the official website. There you can download a zip file with the .exe file, example files and software's manual.

http://cmpg.unibe.ch/software/arlequin35/Arl35Downloads.html

Additionally, you may have also problems with input file. What I usually do is use genealex 6.5 to convert files from genealex to any other software, including Arlequin (option "Export data").

Best regards

 MacClade is not a requirement to use Arlequin.  The instructions you found used MacClade to organize the haplotypes so they could be imported into Arlequin. To me, it sounds like an infile formatting problem.  In my experience with Arlequin, if you have an extra space or tab somewhere that can cause the program not to correctly read your infile.

As Andre mentioned, there are many programs that can convert your files into an alrequin infile.  CREATE and FaBox (http://users-birc.au.dk/biopv/php/fabox/) are a couple more.  

Or you can make the infile yourself.

This may get you started if you have a list of haplotypes already.  If you go through the manual starting on page 28 you can see what all the options are.  I don't have all them listed.

Simple example:

[Profile]

Title="Description of data"

NbSamples=Put number of populations here

DataType=DNA

GenotypicData=put 0  for haplotypic data or  1 for genotypic data

LocusSeparator=NONE

MissingData = "?"

[Data]

[[HaplotypeDefinition]]

HaplListName = EXTERN "list of haplotypes"

HaplList={

H001 GACGC...

H002 GACTA...

}

[[Samples]]

SampleName="Name of population"

SampleSize=XX

SampleData= {

H001 2  [2 indicates that two individuals in this population has Haplotype H001 from the list above]

H002 2

}

SampleName="Name of populations"

SampleSize=XX

SampleData= {

H002 4

}

Hello Sir Robert Wilson, 

I have uploaded my fasta sequences in FaBox. Results show the number of haplotypes so I guess I had that figured out. Thank you!

(1) An Arlequin project file is shown at the bottom. I have made an infile in TextPad, but how do I input this text file in Arlequin? 

(2) In the [[Samples]] section, why do you have two entries of SampleName? If I have samples from 3 different populations, does this mean I will have 3 entries for SampleName? 

Thank you for the time Sir. Highly appreciated!

Hi Sir Andre Lourenco, it seems the GenAlEx is an add-in in Excel. Thank you for the suggestion. I have downloaded it. Will try it out if I fail to create my own infile. :)

When in textPad,  you need to make sure you save with the file extension as .arp and not a .txt.  Also in FaBox, it may not break up your haplotypes by populations and you just may get a list if it has NBSamples = 1.  If that is the case then you have to do some editing of that file using the frequency report to determine how many of each haplotype belongs to each population/group in your dataset or use "the Header field delimiter (2)" setting.

Once you have an .arp file, you can open that file in Arlequin by clicking on "Open Project" and then select your file.  After that you should see your sample/population names in the "project" tab.  Under the "structure" tab you can group your different populations for AMOVAs etc.

Hi Sir Wilson, I think I've got it this time. Thank you so much for your help! I followed the format in your example. I clicked the Start button, and then viewed the results in browser. My next step is to interpret what these results mean. 

Thank you very much to the both of you for helping me initiate this.

Hello everyone. Do I need another software to view the results in Arlequin? I have a problem in viewing the results. Attached is a preview after I clicked View Results in Arlequin. 

I hope you could help me on this. Thank you! 

I am sorry, I do not have experience in Arlequin with sequences. 

It depends on what you want to check, but probably there is something explained in the manual. Another thing that I suggest is to look for papers which done the same analysis that you want.

I always view my results in Internet explorer and then copy/paste the relevant results in notepad or some other program.  I think opening it in a web browser is best instead of opening in Word (if you tell Word it is Unicode for file conversion).  In Word, you can run into the problem of viewing some of the tables  if the table is wider than the sheet of paper. 

My advice is not open the file in Arlequin by clicking view results.  Go into the folder with your results and open up the main.htm file in each of your browsers and see if it improves.  Hopefully either FireFox, Explorer, or Google Chrome will work.  I have tried all three and by default (didn't change any browser settings) my results are displayed in an easy format to read.  I am not sure exactly why yours is not.