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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




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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

[…] 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 […]


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

[…] 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 []., we thank javier suárez, from the federación de arroceros de sevilla, for providing the rice plant seeds, wolfgang dröge-laser for help with rice seed sterilisation, and michael […]


Diversity and microevolution of CRISPR loci in Helicobacter cinaedi

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

[…] 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 []., based on genomic analysis [, ], crispr loci are flanked by cas genes encoding cas proteins (). three cas genes (cas2, cas1 and cas9, in this order) were located […]


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

[…] 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)., polymorphism analysis of the internal transcribed spacer (its) region of the 16s-23s ribosomal dna sequence was performed according […]


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

[…] 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’ […]


Identification of an albumin like protein in plasma of Atlantic cod (Gadus morhua) and its biomarker potential for PAH contamination

PMCID: 5553345
PMID: 28831454
DOI: 10.1016/j.heliyon.2017.e00367

[…] analysis was performed on the atlantic cod albumin-like protein (genscan00000070264) and annotated full-length albumin/albumin-like proteins of other teleost species by clustalx (v. 2.0) and njplot (v. 2.3)., the secondary structure analysis of the atlantic cod albumin-like protein (genscan00000070264) sequence was done by predictprotein (rostlab, available […]

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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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