dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
72 stars 40 forks source link

write_outputs: 3s output format #382

Open isaacovercast opened 4 years ago

isaacovercast commented 4 years ago

It's kind of like phylip. It's closest in format to the gphocs that's written out now, with the full sequence for each locus in blocks. The 3s format only allows for 1 sequence from at most 3 taxa per block, and the sequences can come from mix-and-match individuals within a taxon. This means you'd have to use a pops file, and that it would have to be restricted to 3 populations. It's also not clear how you'd sample sequences from taxa represented by multiple individuals. Randomly? This is non-trivial, and also kind of edge-casey.