ArticleNAR genomics and bioinformatics2020
'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees.
Article in NAR genomics and bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- MELO-ED: learning locality-sensitive multi-embeddings for edit distance.bioRxiv : the preprint server for biology · 2025Article
- An alignment-free method for phylogeny estimation using maximum likelihood.BMC bioinformatics · 2025Article
- Article
- The complexity landscape of viral genomes.GigaScience · 2022Article
- Insertions and deletions as phylogenetic signal in an alignment-free context.PLoS computational biology · 2022Article
- Phylogenies from unaligned proteomes using sequence environments of amino acid residues.Scientific reports · 2022Article
- Space-efficient representation of genomic k-mer count tables.Algorithms for molecular biology : AMB · 2022Article
- Article
- 'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees.NAR genomics and bioinformatics · 2020Article
- Alignment- and reference-free phylogenomics with colored de Bruijn graphs.Algorithms for molecular biology : AMB · 2020Article
- The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances.PloS one · 2020Article
- Benchmarking of alignment-free sequence comparison methods.Genome biology · 2019Article
- Prot-SpaM: fast alignment-free phylogeny reconstruction based on whole-proteome sequences.GigaScience · 2019Article
Corrections and comments
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
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.
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Registered trials
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