have you tried using DnaSp ? I found it very easy and straightforward. Not sure if this is what you are looking for. But I would use DnaSP for such an analysis. 

SHESIS program is available online and has a friendly interface. Even if you want to use other more complex programs, this one (SHESIS) would help you getting the basics (practical) of haplotype analyses.

Available at:  

analysis.bio-x.cn/myAnalysis.php

Hi Rami

No, I can't tell you how to use Haploview or Thesias. But I am trying to guess your question (for the future, it would be nice if you always tell us (i) which kind of data you have, (ii) what kind of analysis you want to perform with these data).

1st possibility: You have allele frequencies of 1 or several populations (microsatellites?). If yes, you could use "Arlequin" (http://cmpg.unibe.ch/software/arlequin35/Arlequin35.html) for statistical analyses. You can calculate, for example, the number of polymorphic sites or the frequency of haplotypes.

2nd possibility: You have aligned sequence data, then you could use DnaSP (http://www.ub.edu/dnasp/). It can read several input files (MEGA, nexus, phylip among others) and it calculates the number of haplotypes, polymorphic sites, gene flow (if you have populations) etc.

Another possibility for aligned sequences is TCS (http://darwin.uvigo.es/software/tcs.html). This program calculates gene genealogies in a network. That means that you get a network, which visualize the relationship between the haplotypes.

I hope I could help you.

best regards

carolina

Dear Carolina

thanks for your response

if I have for example two loci in the same gene

e.x

loci 1                                    loci 2

cc    50                                       aa       45

ct     40                                       ag        45

tt      10                                       gg       10

How can I calculate haplotypes for these genotypes?

Hi Rami

Sorry but I still do not understand your data set.

What I understand: (1) you have 1 gene; (2) 2 loci within the same gene (that means your loci are linked because they are inherited together).

The matrix you show: are these mutations sites within an alignment of sequences? In 50 individuals you have at a certain position "CC", in other 40 individuals the same positions are "CT"? And so one...? And you have both loci in tow different alignments?

If I have guessed correctly, you have two sequence alignments, each of 100 individuals, and within each alignment you found in each case 2 polymorphic sites.

Then use your alignments directly in DnaSP (2nd possibility mentioned above).

Sincerely

Carolina