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Insertions and deletions as phylogenetic signal in an alignment-free context

Niklas Birth, Thomas Dencker, Burkhard Morgenstern
doi: https://doi.org/10.1101/2021.02.03.429685
Niklas Birth
1Department of Bioinformatics, Institute of Microbiology and Genetics, Universe’sät Göttingen, Goldschmidtstr. 1
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Thomas Dencker
1Department of Bioinformatics, Institute of Microbiology and Genetics, Universe’sät Göttingen, Goldschmidtstr. 1
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Burkhard Morgenstern
1Department of Bioinformatics, Institute of Microbiology and Genetics, Universe’sät Göttingen, Goldschmidtstr. 1
2Göttingen Center of Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11
3Campus-Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077 Göttingen, Germany
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  • For correspondence: bmorgen@gwdg.de
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Abstract

Most methods for phylogenetic tree reconstruction are based on sequence alignments; they infer phylogenies from substitutions that may have occurred at the aligned sequence positions. Gaps in alignments are usually not employed as phylogenetic signal. In this paper, we explore an alignment-free approach that uses insertions and deletions (indels) as an additional source of information for phylogeny inference. For a set of four or more input sequences, we generate so-called quartet blocks of four putative homologous segments each. For pairs of such quartet blocks involving the same four sequences, we compare the distances between the two blocks in these sequences, to obtain hints about indels that may have happened between the blocks since the respective four sequences have evolved from their last common ancestor. A prototype implementation is presented to infer phylogenetic trees from these data, using a quartet-tree approach or, alternatively, under the maximum-parsimony paradigm. This approach should not be regarded as an alternative to established methods, but rather as a complementary source of phylogenetic information. Interestingly, however, our software is able to produce phylogenetic trees from putative indels alone that are comparable to trees obtained with existing alignment-free methods.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • We improved the writing to avoid some possible misconceptions.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted September 19, 2021.
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Insertions and deletions as phylogenetic signal in an alignment-free context
Niklas Birth, Thomas Dencker, Burkhard Morgenstern
bioRxiv 2021.02.03.429685; doi: https://doi.org/10.1101/2021.02.03.429685
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Insertions and deletions as phylogenetic signal in an alignment-free context
Niklas Birth, Thomas Dencker, Burkhard Morgenstern
bioRxiv 2021.02.03.429685; doi: https://doi.org/10.1101/2021.02.03.429685

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