I have a list of SNPs from different samples, which present common and different SNPs in respect to a common ancestor. I'm interest to create concatenate files of the SNPs for phylogenetic studies. The problem is that I have samples that don't present a SNPs in a particular position and I need to fill this gap with the reference nucleotide so I obtain perfect concatenate files. This is because if not phylogenetic programs ignore complete this position. I have done it through lockup in excel but when you have more than 30,000 is quite time consuming. Some one knows a better way to do it?