Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

A whole-genome phylogeny of the Escherichia coli/Shigella group was constructed by using the feature frequency profile (FFP) method. This alignment-free approach uses the frequencies of l-mer features of whole genomes to infer phylogenic distances. We present two phylogenies that accentuate differen...

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Veröffentlicht in:Proceedings of the National Academy of Sciences - PNAS 2011-05, Vol.108 (20), p.8329-8334
Hauptverfasser: Sims, Gregory E, Kim, Sung-Hou
Format: Artikel
Sprache:eng
Schlagworte:
Biological Evolution
Biological Sciences
Commensals
Convergent evolution
Divergent evolution
E coli
Escherichia coli
Escherichia coli - genetics
Evolution
genome
Genome, Bacterial
Genomes
Genomics
Gram-negative bacteria
interspersed repetitive sequences
Models, Genetic
pathogens
Phylogenetics
Phylogeny
Physical Sciences
Plasmids
Shigella
Shigella - genetics
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Zusammenfassung:A whole-genome phylogeny of the Escherichia coli/Shigella group was constructed by using the feature frequency profile (FFP) method. This alignment-free approach uses the frequencies of l-mer features of whole genomes to infer phylogenic distances. We present two phylogenies that accentuate different aspects of E. coli/Shigella genomic evolution: (i) one based on the compositions of all possible features of length l = 24 (
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.1105168108