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  Fast phylogeny reconstruction from genomes of closely related microbes

Haubold, B., & Klötzl, F. (2021). Fast phylogeny reconstruction from genomes of closely related microbes. In A. Mengoni, G. Bacci, & M. Fondi (Eds.), Bacterial Pangenomics: Methods in Molecular Biology (pp. 77-89). New York, NY: Springer US. doi:10.1007/978-1-0716-1099-2_6.

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Item Permalink: https://hdl.handle.net/21.11116/0000-000C-B5F0-8 Version Permalink: https://hdl.handle.net/21.11116/0000-000C-B5F1-7
Genre: Book Chapter

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978-1-0716-1099-2_6.pdf (Publisher version), 932KB
 
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2021
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 Creators:
Haubold, Bernhard1, Author           
Klötzl, Fabian1, Author           
Affiliations:
1Research Group Bioinformatics, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445644              

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Free keywords: Genomic epidemiology; Phylogeny; Support values; Homology; Maximal match; Distance matrix
 Abstract: By tracking pathogen outbreaks using whole genome sequencing, medical microbiology is currently being transformed into genomic epidemiology. This change in technology is leading to the rapid accumulation of large samples of closely related genome sequences. Summarizing such samples into phylogenies can be computationally challenging. Our program andi quickly computes accurate pairwise distances between up to thousands of bacterial genomes. Working under the UNIX command line, we show how andi can be used to transform genomes to phylogenies with support values ready to be printed or integrated into documents.

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Language(s): eng - English
 Dates: 20212021
 Publication Status: Issued
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1007/978-1-0716-1099-2_6
 Degree: -

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Title: Bacterial Pangenomics: Methods in Molecular Biology
Source Genre: Book
 Creator(s):
Mengoni, Alessio, Editor
Bacci, Giovanni, Editor
Fondi, Marco, Editor
Affiliations:
-
Publ. Info: New York, NY : Springer US
Pages: - Volume / Issue: 2242 (Chapter 6) Sequence Number: - Start / End Page: 77 - 89 Identifier: ISSN: 1064-3745
ISSN: 1940-6029
ISBN: 978-1-0716-1098-5
ISBN: 978-1-0716-1099-2