@article{dencker_leimeister_gerth_bleidorn_snir_morgenstern_2019,
title={'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees},
volume={2},
DOI={10.1093/nargab/lqz013},
abstractNote={Abstract
Word-based or 'alignment-free' methods for phylogeny inference have become popular in recent years. These methods are much faster than traditional, alignment-based approaches, but they are generally less accurate. Most alignment-free methods calculate 'pairwise' distances between nucleic-acid or protein sequences; these distance values can then be used as input for tree-reconstruction programs such as neighbor-joining. In this paper, we propose the first word-based phylogeny approach that is based on 'multiple' sequence comparison and 'maximum likelihood'. Our algorithm first samples small, gap-free alignments involving four taxa each. For each of these alignments, it then calculates a quartet tree and, finally, the program 'Quartet MaxCut' is used to infer a super tree for the full set of input taxa from the calculated quartet trees. Experimental results show that trees produced with our approach are of high quality.},
number={1},
publisher={Oxford University Press (OUP)},
author={Dencker, Thomas and Leimeister, Chris-André and Gerth, Michael and Bleidorn, Christoph and Snir, Sagi and Morgenstern, Burkhard},
year={2019},
month={Oct}
}