bcgTree specifications

Information


Unique identifier OMICS_26727
Name bcgTree
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, Perl
License MIT License
Computer skills Advanced
Version 1.0.10
Stability Stable
Maintained Yes

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Versioning


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Documentation


Maintainers


  • person_outline Markus J. Ankenbrand
  • person_outline Alexander Keller

Publication for bcgTree

library_books

BcgTree: automatized phylogenetic tree building from bacterial core genomes.

2016 Genome
PMID: 27603265
DOI: 10.1139/gen-2015-0175

bcgTree citations

 (2)
library_books

Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain Specific Genes and Resolves Metagenomics Data Down to the Strain Level

2018
Front Microbiol
PMCID: 5797582
PMID: 29441050
DOI: 10.3389/fmicb.2018.00063

[…] s subsp. subtilis str. 168 as outgroup. The predicted CDSs of all strains, including the three L. helveticus strains of this study, were used to calculate a maximum likelihood phylogenetic tree using bcgTree (Ankenbrand and Keller, ), which uses HMM models of 107 known housekeeping genes (Dupont et al., ). bcgTree was parameterized to perform 100 bootstrap runs while executing RAxML (Stamatakis, ) […]

library_books

Draft Genome Sequence of the Nitrogen Fixing Rhizobium sullae Type Strain IS123T Focusing on the Key Genes for Symbiosis with its Host Hedysarum coronarium L.

2017
Front Microbiol
PMCID: 5526965
PMID: 28798728
DOI: 10.3389/fmicb.2017.01348

[…] of the Rhizobiales was carried out to extract the core pan-genome, which was aligned with the genomes of the other rhizobia and scored for conservation percentage. The analysis was carried out using bcgTree, which is a bacterial core gene analyzer (http://www.dna-analytics.biozentrum.uni-wuerzburg.de, Ankenbrand and Keller, ). […]

bcgTree institution(s)
Department of Animal Ecology and Tropical Biology, University of Wurzburg, Wurzburg, Germany
bcgTree funding source(s)
Supported by a grant of the German Excellence Initiative to the Graduate School of Life Sciences, University of Würzburg.

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