I am working with PopArt (Population Analysis with Reticulate Trees) software making statistical parsimony haplotype networks. It uses nexus format, and I had not trouble formatting and making a single color network, but am struggling a bit with importing and applying the traits block or instruction file, my goal is to produce a network with color coded sampling regions or populations. Can anyone share an example traits file that's correctly formatted to indicate color in the network by population or geographic sampling location? Many thanks, Brenden
Hi Brendon, I think I can help you with that. I have a little bit of experience in creating haplotype network with PopArt. I have attached a few images for reference. First of all, you will need to open your nex file in notepad where you will see your sequence names under taxalabels (fig 1) followed by sequence characters and so on. Go to the end (fig 2) where you need to add your traits in a code format (fig 3). Here,you have to use binary code-0(absent) or 1 (present). For example, two Genotype 1A are present in South_24_PGS (a geographic location) so i put 1 under that region for each sequence, keeping the rest 0. Next two genotype 1A were present in South_Kolkata so i put 1 in each case under that area. You have to code for each sequence this way and finally you have to put an end command (fig 4). Now save and open this new nex file with popart. You will have the traits attributed to each haplotypes. Hope this helps.
@Ajanta, thank you for your detailed message. I'll take a look now!
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