Best systematist practice transferred to molecular data

Abstract In the first part of the paper, we give a short description of the “minimum conflict” phylogeny estimation algorithm that analyzes molecular data in a way that resembles traditional best practice in morphological systematics. The algorithm calculates the tree from the root to the leaves, focussing on the detection of shared novel (synapomorphic) character states. Following the encaptic order of monophyla, at each step an outgroup serves to distinguish shared novel from shared old character states. The group of species under consideration is split in such a way that no synapomorphies of subgroups are torn apart, indicating that the split divides the group into two monophyla. In the second part of the paper, we describe the validation of our method with both natural and artificial data. Our method is very fast in theory, enabling the analysis of large quantities of data on a genomic scale. A Perl prototype is available on the World-Wide Web, via http://bibiserv.techfak.uni-bielefeld.de/mcope/ .