I would like to use PopART software for creating haplotype network. When I tried to upload the alignment of 50 sequences by inserting alignment?
may i know what may be the reason
Hi Dilini, I guess the easiest way is to begin with DNASP. With your FASTA file, use DNASP programme to define your sequences (here I mean either sampling localities or populations) and then export your haplotype data (arlequin format) containing only variable positions. Then you have to 'manually' prepare two infiles as follows: XXXX.hap (this is the one you generated with DNASP), and XXXX.nexus (this you could edit from previous files like the one I have attached). To skip details I have attached my previous files which you could easily use to create yours. I hope this is helpful!
you cannot just enter the alignment into the sample file i in the PopArt manual.
You first need to have a list of unique haplotypes that you will use (FASTA).
You also need to have a Nexus file generated (mostly easily through DnaSP).
You then need to put the appropriate traits block with the correct matrix corresponding to you sequences.
If that helps, hard to tell with the question in its current state.
Similar questions, have been asked on RG before. Have a look around.
Without detail its hard to help... I do have a Python script which writes the PopArt block to your Nexus file which may help. You can find it on my github: https://github.com/tkchafin/scripts, so assuming that your issue is with creating a proper input file, this may or may not be helpful.
Hi Dilini, I guess the easiest way is to begin with DNASP. With your FASTA file, use DNASP programme to define your sequences (here I mean either sampling localities or populations) and then export your haplotype data (arlequin format) containing only variable positions. Then you have to 'manually' prepare two infiles as follows: XXXX.hap (this is the one you generated with DNASP), and XXXX.nexus (this you could edit from previous files like the one I have attached). To skip details I have attached my previous files which you could easily use to create yours. I hope this is helpful!
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