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NJplot specifications

Information


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

 (159)
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Primordial origin and diversification of plasmids in Lyme disease agent bacteria

2018
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 […]

call_split

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

2018
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 []. […]

call_split

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

2017
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 ). […]

library_books

Diversity and microevolution of CRISPR loci in Helicobacter cinaedi

2017
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 []. […]

call_split

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

2017
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). […]

library_books

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

2017
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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