Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression

Karel Břinda; Leandro Lima; Simone Pignotti; Natalia Quinones-Olvera; Kamil Salikhov; Rayan Chikhi; Gregory Kucherov; Zamin Iqbal; Michael Baym

doi:10.1101/2023.04.15.536996

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Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression

View ORCID ProfileKarel Břinda, View ORCID ProfileLeandro Lima, Simone Pignotti, View ORCID ProfileNatalia Quinones-Olvera, Kamil Salikhov, View ORCID ProfileRayan Chikhi, View ORCID ProfileGregory Kucherov, View ORCID ProfileZamin Iqbal, View ORCID ProfileMichael Baym

doi: https://doi.org/10.1101/2023.04.15.536996

Karel Břinda

1Inria, Irisa, Univ. Rennes, 35042 Rennes, France

2Department of Biomedical Informatics, Harvard Medical School, MA 02115 Boston, USA

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For correspondence: karel.brinda@inria.fr baym@hms.harvard.edu

Leandro Lima

3EMBL-EBI, CB10 1SD Hinxton, UK

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Simone Pignotti

2Department of Biomedical Informatics, Harvard Medical School, MA 02115 Boston, USA

4LIGM, CNRS, Univ. Gustave Eiffel, 77454 Marne-la-Vallée, France

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Natalia Quinones-Olvera

2Department of Biomedical Informatics, Harvard Medical School, MA 02115 Boston, USA

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Kamil Salikhov

4LIGM, CNRS, Univ. Gustave Eiffel, 77454 Marne-la-Vallée, France

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Rayan Chikhi

5Institut Pasteur, Univ. Paris Cité, G5 Sequence Bioinformatics, 75015 Paris, France

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Gregory Kucherov

4LIGM, CNRS, Univ. Gustave Eiffel, 77454 Marne-la-Vallée, France

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Zamin Iqbal

3EMBL-EBI, CB10 1SD Hinxton, UK

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Michael Baym

2Department of Biomedical Informatics, Harvard Medical School, MA 02115 Boston, USA

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For correspondence: karel.brinda@inria.fr baym@hms.harvard.edu

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https://brinda.eu/mof
https://github.com/karel-brinda/MiniPhy
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Posted May 11, 2024.

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Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression

Karel Břinda, Leandro Lima, Simone Pignotti, Natalia Quinones-Olvera, Kamil Salikhov, Rayan Chikhi, Gregory Kucherov, Zamin Iqbal, Michael Baym

bioRxiv 2023.04.15.536996; doi: https://doi.org/10.1101/2023.04.15.536996

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Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression

Karel Břinda, Leandro Lima, Simone Pignotti, Natalia Quinones-Olvera, Kamil Salikhov, Rayan Chikhi, Gregory Kucherov, Zamin Iqbal, Michael Baym

bioRxiv 2023.04.15.536996; doi: https://doi.org/10.1101/2023.04.15.536996

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