text: user2680: Currently my lab manually uses pop art to make the network after using PHASE to id an individual's alleles. I would like to know how to generate the graph structure (i.e. the links between vertices), as well as how to draw the graph.
  Input data are formatted as FASTA files with the sequence in nucleotide formatting.
  Example:
  
  
  I just feel like there's got to be a better, more time effective way to do this.
  
  user3848: This is a haplotype map, where each node is proportional to the frequency of a given allele. The formal tool to do this is Network 5 found here. The problem with manaul haplotype maps is the area of the node should be proportional to the frequency, if this is not accurate it could be perceived to be misleading. 
  The approach for looking at each parsimonious state along a branch is a phylogenetics method which is performed via MacClade 4.0 ... requires an old Mac though.
  
original_text: 2680: <p>Currently my lab manually uses pop art to make the network after using PHASE to id an individual's alleles. I would like to know how to generate the graph structure (i.e. the links between vertices), as well as how to draw the graph.</p>
  <p>Input data are formatted as FASTA files with the sequence in nucleotide formatting.</p>
  <p>Example:
  <a href="https://i.stack.imgur.com/nnRTj.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/nnRTj.jpg" alt="network of alleles" /></a>
  <a href="https://i.stack.imgur.com/CR8Dh.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/CR8Dh.jpg" alt="Network  in black and white of groups of alleles" /></a>
  I just feel like there's got to be a better, more time effective way to do this.</p>
   3848: <p>This is a haplotype map, where each node is proportional to the frequency of a given allele. The formal tool to do this is Network 5 found <a href="http://www.fluxus-engineering.com/sharenet.htm" rel="nofollow noreferrer">here</a>. The problem with manaul haplotype maps is the area of the node should be proportional to the frequency, if this is not accurate it could be perceived to be misleading. </p>
  
  <p>The approach for looking at each parsimonious state along a branch is a phylogenetics method which is performed via MacClade 4.0 ... requires an old Mac though.</p>
  