I just discovered the popART software, usually i analyze haplotype network using NETWORK software but some reviewer request me to use this software. however im stuck at how to determine the traits of my sequences. i tried using DNAsp software and found 143 traits for my sequences but i still does not know how to export it into .nex and used it in popArt software. can anyone help me .
Hello Mohamad,
I don't know if you have already find steps to establish your network in Popart. However, here are steps to follow:
- Initially, use DNAsp software to convert your fasta to nexus file : open data file, check Format , go to Generate then Haplotype data file then Nexus Haplotype data file,
Or you can use the link below to convert your fasta file to sequential nexus file format:
https://www.hiv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html
- Open your downloded nexus file with notepad or blocknote
- Add at the end of the file the traits like this example:
Begin Traits;
Dimensions NTraits=4;
Format labels=yes missing=? separator=Comma;
TraitLabels Hajera Laou Loukkos Tangerois;
Matrix
Hap_1 0,0,1,0
Hap_2 0,0,1,0
Hap_3 12,12,22,1
Hap_4 0,0,1,0
Hap_5 0,0,2,0
Hap_6 0,0,1,0
Hap_7 10,22,1,15
Hap_8 0,0,3,0
Hap_9 0,1,11,0
Hap_10 0,0,2,0
Hap_11 0,0,1,0
Hap_12 0,1,0,0
Hap_13 0,1,0,0
Hap_14 0,1,0,0
Hap_15 0,1,0,0
Hap_16 0,0,0,1
Hap_17 0,0,0,2
Hap_18 0,0,0,2
;
End;
Ntraits: number of locations/populations you have (4 in my example)
Traitlabels : name of locations
The matrix : haplotypes sequences (18 haplotypes here), the numbers next related to (how many haplotypes in each location) where the arrangement must be as the arrangement of the trait label above
For example Hap_3 12,12,22,1 means that we found 12 of Hap_3 in Hajera, 12 in Laou, 22 loukkos, 1 Tangerois
Your nexus file is now ready for popart software,Open popart and:
File> open all files > open your edited sequential nexus file.
Finally, select the desired network and, if preferred, change its color.
I know how to use the network software but not using PopART software
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