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NJplot specifications


Unique identifier OMICS_04815
Name NJplot
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Stability Stable
Maintained Yes




No version available

Publication for NJplot

NJplot citations


Primordial origin and diversification of plasmids in Lyme disease agent bacteria

BMC Genomics
PMCID: 5870499
PMID: 29580205
DOI: 10.1186/s12864-018-4597-x
call_split See protocol

[…] otide and protein sequence alignments were performed by BLASTn and BLASTp [], ClustalX [] and DNA Strider []. Neighbor-joining trees were created by ClustalX [], and the resulting trees were drawn by NJPlot (http://pbil.univ-lyon1.fr/software/njplot.html). Maximum likelihood trees were inferred with RAxML []. Determination of percent identity between chromosomes was determined through reference-in […]


Protein Activity of the Fusarium fujikuroi Rhodopsins CarO and OpsA and Their Relation to Fungus–Plant Interaction

Int J Mol Sci
PMCID: 5796164
PMID: 29324661
DOI: 10.3390/ijms19010215
call_split See protocol

[…] of Gibberella zeae []. The bootstrap NJ tree was obtained with the ClustalX 1.83 program [], excluding gaps, and applying the correction for multiple substitutions. The tree was represented with the NJPlot program []. […]


Regular Wounding in a Natural System: Bacteria Associated With Reproductive Organs of Bedbugs and Their Quorum Sensing Abilities

Front Immunol
PMCID: 5741697
PMID: 29326722
DOI: 10.3389/fimmu.2017.01855
call_split See protocol

[…] g of the sequences and ClustalX for the sequence alignment. The Maximum Likelihood phylogenetic tree of the bacterial sequences was determined by using the web interface RAxML Black Box (Figure ) and NJplot to draw the phylogenetic tree (Figure ). […]


Diversity and microevolution of CRISPR loci in Helicobacter cinaedi

PLoS One
PMCID: 5640232
PMID: 29028814
DOI: 10.1371/journal.pone.0186241

[…] imated by concatenated sequences using the neighbor-joining method []. Clustal X software was used to align the sequences [], and calculate the genetic distances. The dendrogram was constructed using NJplot program [] and MEGA 6 []. […]


Evaluation of repetitive PCR and matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI TOF MS) for rapid strain typing of Bacillus coagulans

PLoS One
PMCID: 5636150
PMID: 29020109
DOI: 10.1371/journal.pone.0186327
call_split See protocol

[…] a.prabi.fr/software/seaview). Bootstrap values were calculated by the neighbor-joining method [] using ClustalX2. The phylogenetic tree based on the ClustalX2 analysis was displayed using open-source NJplot software (http://doua.prabi.fr/software/njplot). […]


Population structure of sea type and lake type sockeye salmon and kokanee in the Fraser River and Columbia River drainages

PLoS One
PMCID: 5590831
PMID: 28886033
DOI: 10.1371/journal.pone.0183713

[…] nifing over loci. Cavalli-Sforza and Edwards chord distance (CSE) [] was used to estimate genetic distances among all populations. An unrooted neighbor-joining tree based upon CSE was generated using NJPLOT []. Bootstrap support for the major nodes in the tree was evaluated with the CONSENSE program from PHYLIP based upon 500 replicate trees []. FSTAT was used to measure the ‘allelic richness’ (al […]


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NJplot institution(s)
Laboratoire de Biométrie, Génétique et Biologie des Populations, Université Claude-Bernard Lyon-1, Villeurbanne, France

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