Workflow of the full AMY-tree software package. The input of AMY-tree are the called Y-SNPs for an individual under study, a Y chromosomal phylogenetic tree, mutation conversion data of all known Y-SNPs and the reference genome. In the algorithm, AMY-tree checks first the quality of the called Y-SNPs via the ‘Call quality test’. Then, vertical and horizontal methods are applied to assign the sub-haplogroup of the sample and their results are combined to get the combinatorial result. In order to remove more false positive results, the most specific result is retained and returned as final result. The output of AMY-tree is the analysis file with the assignment of the sub-haplogroup for the sample and three files which make it possible to check, correct and expand the phylogenetic tree.