These are chat archives for dereneaton/ipyrad
I am looking over the .loci file from the output and comparing that to other output files. In the .loci file, you list “-“ as phylogenetically uninformative and “” as phylogenetically informative. From my .loci file, I count:
3672 loci in the file
297 loci contain neither - nor
264 loci with ONLY - (NO phylogenetically informative sites *)
3111 loci containing at least one phylogenetically informative site
My .stru file, HOWEVER, contains 3375 snps. That’s equivalent to the total 3672 loci - 297 sites with neither - nor *.
Hence, of my 3375 snps, 264 of them include uninformative snps! Does that mean when you randomly grab snps for the .stru file, that you are grabbing the phylogenetically uninformative sites (even when * is an option for a given locus) such that I could have many more than 264 uninformative snps???