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Motivation: Word-based or `alignment-free' methods for phylogenyreconstruction are much faster than traditional approaches, but they aregenerally less accurate. Most of these methods calculate pairwise distances fora set of input sequences, for example from word frequencies, from so-calledspaced-word matches or from the average length of common substrings.  Results: In this paper, we propose the first word-based approach to treereconstruction that is based on multiple sequence comparison and MaximumLikelihood. Our algorithm first samples small, gap-free alignments involvingfour taxa each. For each of these alignments, it then calculates a quartet treeand, finally, the program Quartet MaxCut is used to infer a super tree topologyfor the full set of input taxa from the calculated quartet trees. Experimentalresults show that trees calculated with our approach are of high quality.  Availability: The source code of the program is available athttps://github.com/tdencker/multi-SpaM  Contact: thomas.dencker@stud.uni-goettingen.de

Multi-SpaM: a Maximum-Likelihood approach to Phylogeny reconstruction based on Multiple Spaced-Word Matches