I'm trying to produce a haplotype network and so have decided to use the software haploview. However I'm having some problems importing my sequences into the software.

I Have my sequences in a FASTA format but I can't find a way to convert this into a format that haploview accepts.

Does anyone have any ideas how I can get from a FASTA format file (e.g. >Az01|Female|Azores AGGATCT...) to a phased haplotype format (Az01 Azores 0 4 2 2)?

  • $\begingroup$ You should let us know how your fasta files are like. What is your reference etc? These are the reads or assembled genomes? $\endgroup$ – WYSIWYG Dec 19 '14 at 13:19
  • $\begingroup$ @Luigi Collapser would just collapse redundant reads to a single sequence. $\endgroup$ – WYSIWYG Dec 19 '14 at 15:12
  • $\begingroup$ Shoot, I linked to the wrong tool! $\endgroup$ – Luigi Dec 19 '14 at 15:13
  • $\begingroup$ What are your sequences? PED format is for SNP data, but I suspect you have a single gene. $\endgroup$ – alephreish Dec 19 '14 at 17:36
  • $\begingroup$ I'm rather new to bioinformatics, so please excuse me if I'm a bit slow. They are reads of the ITS region of a shark species, and they're 910 bps long. I did produce a haplotype diagram in TCS, but I was told haploview was better. I'm looking at haplotypes from different geographic regions. $\endgroup$ – Will Perry Dec 19 '14 at 19:14

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