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BIONJ specifications

Information


Unique identifier OMICS_20669
Name BIONJ
Alternative name Bio neighbor-joining

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This tool is not maintained anymore.

Publication for Bio neighbor-joining

BIONJ citations

 (240)
call_split

Genomic and functional characterisation of IncX3 plasmids encoding blaSHV 12 in Escherichia coli from human and animal origin

2018
Sci Rep
PMCID: 5955891
PMID: 29769695
DOI: 10.1038/s41598-018-26073-5
call_split See protocol

[…] were used to determine the presence of resistance genes, replicon types and insertion sequences, respectively–. Plasmid sequences were hierarchically clustered and displayed as a phenogram using the BioNJ algorithm, where the underlying distance matrix was calculated from the pairwise non-overlapping maximal unique matches (MUMs) using Nucmer version 3.07,. Relative pairwise distances were obtain […]

call_split

Fluorescent reporter lines for auxin and cytokinin signalling in barley (Hordeum vulgare)

2018
PLoS One
PMCID: 5918912
PMID: 29694399
DOI: 10.1371/journal.pone.0196086
call_split See protocol

[…] iated taxa clustered together in the bootstrap test (100 replicates) are shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. […]

library_books

Inferring the Minimal Genome of Mesoplasma florum by Comparative Genomics and Transposon Mutagenesis

2018
mSystems
PMCID: 5893858
PMID: 29657968
DOI: 10.1128/mSystems.00198-17

[…] roduce a sequence matrix of 138,476 amino acid sites. Both phylogenetic trees ( and ) were made from this alignment with SeaView (v.4.6.1) (). The distance tree was generated by neighbor joining with BIONJ () and the Kimura distance model (). The maximum-likelihood tree was generated with PhyML (v3.0) () and the LG evolutionary model (). Bootstrap values were calculated by using 100 regular bootst […]

library_books

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

2018
Wellcome Open Res
PMCID: 5930550
PMID: 29774245
DOI: 10.21956/wellcomeopenres.15526.r32391

[…] ociation of epidemiological traits (for example a switch in location of isolation) a more precise topology may then be desired.We also directly compared a range of evolutionary models, run both using BIONJ and ML ( ; ). As there are a huge number of sites, and the sites are each low-dimensional, we are much better informed about the site evolution model than the tree. It’s easier to get the tree w […]

call_split

Routine Whole Genome Sequencing for Outbreak Investigations of Staphylococcus aureus in a National Reference Center

2018
Front Microbiol
PMCID: 5869177
PMID: 29616014
DOI: 10.3389/fmicb.2018.00511
call_split See protocol

[…] ent in all the isolates to be compared and aligned their sequences using () gene by gene. Aligned core-gene sequences were then concatenated into a final alignment and we used FastTree v1 () with the BIONJ algorithm () to infer the phylogeny. EpiSeqTM V1 also extracted the number of SNP in each specific core gene alignment. It calculates the number of single nucleotide differences in the alignment […]

library_books

Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014–15

2018
PMCID: 5823344
PMID: 29460729
DOI: 10.3201/eid2403.171499

[…] e/seaview) with a general time-reversible model and approximate likelihood ratio test branch support, where the tree with the greatest log likelihood was retained. We generated initial trees by using BioNJ () with optimized tree topology. We used FigTree version 1.4.2 (http://tree.bio.ed.ac.uk/) to manipulate the phylogenetic trees and to root to the outgroup influenza A(H3N2) isolate from Switzer […]

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BIONJ institution(s)
GERAD, Ecole des HEC, Montreal, Quebec, Canada

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