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Inferring Core Genome Phylogenies for Bacteria

Part of the Methods in Molecular Biology book series (MIMB,volume 2242)

Abstract

Due to the increasing availability of public bacterial genome data and cost efficiency of novel bacterial strain sequencing, phylogenetic analyses based on more than a single or few marker genes have become feasible. In this method protocol, we describe the complete bioinformatic workflow from raw genomic data to final phylogenetic analyses based on 107 conserved single copy genes. This approach can be used to perform phylogenetic reconstructions with high resolution on strain level or across taxa spanning different clades of the bacterial tree of life.

Key words

  • Phylogenetics
  • Phylogenomics
  • Prokaryote
  • 16S
  • Genomics
  • Bioinformatics
  • Sequence analysis
  • Maximum likelihood
  • High-performance computing
  • Parallel computing

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  • DOI: 10.1007/978-1-0716-1099-2_4
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Correspondence to Alexander Keller .

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Keller, A., Ankenbrand, M.J. (2021). Inferring Core Genome Phylogenies for Bacteria. In: Mengoni, A., Bacci, G., Fondi, M. (eds) Bacterial Pangenomics. Methods in Molecular Biology, vol 2242. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1099-2_4

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  • DOI: https://doi.org/10.1007/978-1-0716-1099-2_4

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1098-5

  • Online ISBN: 978-1-0716-1099-2

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