HPC: Hierarchical phylogeny construction.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2019
2019
Historique:
received:
06
03
2019
accepted:
05
08
2019
entrez:
23
8
2019
pubmed:
23
8
2019
medline:
5
3
2020
Statut:
epublish
Résumé
Rapid improvements in DNA sequencing technology have resulted in long genome sequences for a large number of similar isolates with a wide range of single nucleotide polymorphism (SNP) rates, where some isolates can have thousands of times lower SNP rates than others. Genome sequences of this kind are a challenge to existing methods for construction of phylogenetic trees. We address the issues by developing a hierarchical approach to phylogeny construction. In this method, the construction is performed at multiple levels, where at each level, groups of isolates with similar levels of similarity are identified and their phylogenetic trees are constructed. Time savings are achieved by using a sufficiently large number of columns from the input alignment, instead of all its columns. Our results show that the new approach is 20-60 times more efficient than existing programs and more accurate in situations where highly similar isolates have a wide range of SNP rates.
Identifiants
pubmed: 31437210
doi: 10.1371/journal.pone.0221357
pii: PONE-D-19-06578
pmc: PMC6705828
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0221357Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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