@dereneaton I am analizing some 150bp PE ddRAD data of one species of primate for some population genetic analysis. After running s1-7 I realized that many of my loci have this weird pattern, where iPYRAD identifies a SNP per each site of the last ~40bp of the loci. After looking at the data, I realized that is due to the fact that there was an incomplete digestion of the restriction enzyme in some samples. Given the fact that I have a very common enzyme not all reads are cut at the same site, and for some loci I observe two very proximate RE sites which leads to a weird alignment of the end of the loci and thus the identification of many fake SNPS. I was wondering if in iPYRAD is there any way of adaptitively trimming the loci so that the last bp of the loci are eliminated not simply on default value (using trim loci) but if like in PYRAD, loci could be trimmed to the shortest read? Thanks!!