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Protocols

Gegenees specifications

Information


Unique identifier OMICS_15881
Name Gegenees
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 2.2.1
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Bo Segerman

Publication for Gegenees

Gegenees citations

 (50)
library_books

Genomic Architecture of the Two Cold Adapted Genera Exiguobacterium and Psychrobacter: Evidence of Functional Reduction in the Exiguobacterium antarcticum B7 Genome

2018
Genome Biol Evol
PMCID: 5833320
PMID: 29438502
DOI: 10.1093/gbe/evy029

[…] Tree v.4.14.2 () to obtain an unrooted tree. In the second approach, the whole nucleotide sequence of the genomes, including their plasmids, were compared all-against-all by BLASTn using the software Gegenees v.2.2.1 () with a fragment size of 200 bp and a step size of 100 bp. Fragments with identity values >30% were used to calculate the similarity scores. The result was presented as a heat map w […]

library_books

Large scale genomic analyses reveal the population structure and evolutionary trends of Streptococcus agalactiae strains in Brazilian fish farms

2017
Sci Rep
PMCID: 5648781
PMID: 29051505
DOI: 10.1038/s41598-017-13228-z

[…] The similarity of whole genomes were compared using Gegenees software version 2.0 along with other piscine S. agalactiae strains that had complete genome sequences, 138spar (ST-261) and GD201008-001 (ST-7) (GenBank access numbers CP007565 and CP003810, […]

library_books

New Insights into the Diversity of the Genus Faecalibacterium

2017
Front Microbiol
PMCID: 5609107
PMID: 28970823
DOI: 10.3389/fmicb.2017.01790

[…] and the diversity inside genus Faecalibacterium.A whole-genome comparative analysis further validated our findings from the 16S rRNA gene phylogeny. A whole-genome similarity matrix was obtained with Gegenees software and used for a phylogenomic analysis; the resulting phylogenetic tree agreed with the previously performed 16S rRNA analysis in identifying the same three groups of strains: clusters […]

library_books

Phylogenomics of Colombian Helicobacter pylori isolates

2017
PMCID: 5594506
PMID: 28912838
DOI: 10.1186/s13099-017-0201-1

[…] The genomes sequenced in this study were aligned with 34 H. pylori reference strains from the National Center for Biotechnology Information (NCBI) databases using the Gegenees v2.21 tool. This tool uses an algorithm to align genomic fragments and compares them by Blastn [, ]. The fragment size was 200 bp, and the sliding step size was 100 bp. The average sequence s […]

call_split

Identification and genomic comparison of temperate bacteriophages derived from emetic Bacillus cereus

2017
PLoS One
PMCID: 5590980
PMID: 28886124
DOI: 10.1371/journal.pone.0184572
call_split See protocol

[…] m known transcription factor binding sites were identified using Bprom (http://linux1.softberry.com/berry.phtml). Comparative genome analysis of the phages at the nucleotide level was conducted using Gegenees 2.1 (window size of 50 bp, step-size of 25 bp, and cutoff of 30%) and Mauve, and comparison at the proteomic level was made using CoreGenes 3.0 (http://binf.gmu.edu:8080/CoreGenes3.0). Genes […]

library_books

The Mobilome; A Major Contributor to Escherichia coli stx2 Positive O26:H11 Strains Intra Serotype Diversity

2017
Front Microbiol
PMCID: 5592225
PMID: 28932209
DOI: 10.3389/fmicb.2017.01625

[…] er (http://phaster.ca/). This application outputs a fasta file containing all predicted prophage regions (the “phageome”) for each isolate. The global “phageome” of all strains was compared using the Gegenees software (see above). The predicted prophage regions were then pairwise compared using the progressive Mauve alignment tool, EasyFig (Sullivan et al., ) and Blastn. […]

Citations

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Gegenees institution(s)
Department of Bacteriology, National Veterinary Institute (SVA), Uppsala, Sweden; Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
Gegenees funding source(s)
This work was supported by the Swedish Civil Contingencies Agency, by the European Union funded Integrated Project BIOTRACER (contract 036272) under the 6th RTD Framework and by/executed in the framework of the EU-project AniBioThreat (Grant Agreement: Home/2009/ISEC/AG/191) with the financial support from the Prevention of and Fight against Crime Programme of the European Union, European Commission-Directorate General Home Affairs.

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