{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/multi-spam-a-maximum-likelihood-approach-to","title":"Multi-SpaM: a Maximum-Likelihood approach to Phylogeny reconstruction based on Multiple Spaced-Word Matches","arxiv_id":"1803.09222","date":"2018-04-28","proceeding":null,"authors":[],"abstract":"Motivation: Word-based or `alignment-free' methods for phylogeny\nreconstruction are much faster than traditional approaches, but they are\ngenerally less accurate. Most of these methods calculate pairwise distances for\na set of input sequences, for example from word frequencies, from so-called\nspaced-word matches or from the average length of common substrings.\n  Results: In this paper, we propose the first word-based approach to tree\nreconstruction that is based on multiple sequence comparison and Maximum\nLikelihood. Our algorithm first samples small, gap-free alignments involving\nfour taxa each. For each of these alignments, it then calculates a quartet tree\nand, finally, the program Quartet MaxCut is used to infer a super tree topology\nfor the full set of input taxa from the calculated quartet trees. Experimental\nresults show that trees calculated with our approach are of high quality.\n  Availability: The source code of the program is available at\nhttps://github.com/tdencker/multi-SpaM\n  Contact: thomas.dencker@stud.uni-goettingen.de","url_abs":"http://arxiv.org/abs/1803.09222v2","url_pdf":"http://arxiv.org/pdf/1803.09222v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"multi-spam-a-maximum-likelihood-approach-to","repo_url":"https://github.com/tdencker/multi-SpaM","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}