NJplot protocols

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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 No

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Publication for NJplot

NJplot in pipelines

 (28)
2017
PMCID: 5640232
PMID: 29028814
DOI: 10.1371/journal.pone.0186241

[…] 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 […]

2016
PMCID: 4775529
PMID: 27087922
DOI: 10.1002/ece3.1951

[…] tree was constructed using clustalx with neighbor‐joining method maximum likelihood, and then validated by using 1000 bootstrap replicates in clustalx. the phylogenetic trees were presented using njplot (perrière and gouy )., figure  shows average pairwise p‐distance in each taxonomic group of bacteria, which cover 14 phyla, 29 classes, 66 orders, 142 families, and 463 genera. figure  […]

2016
PMCID: 4856094
PMID: 26994288
DOI: 10.1534/g3.115.026104

[…] protein sequences were aligned with clustalw () at the dna data bank of japan website (ddbj; http://www.ddbj.nig.ac.jp/search/clustalw-e.html). a phylogenetic tree was generated with njplot software (http://doua.prabi.fr/software/njplot; )., mature leaves of 2-month-old plants were cut into 3-mm strips and placed on 2% agar plates at 28°. the leaf strips were analyzed […]

2016
PMCID: 4978470
PMID: 27505001
DOI: 10.1371/journal.pone.0160554

[…] were further used to build a multiple alignment with mafft-7.187 []. newick formula was obtained by submitting the mafft output file to fasttree-2.1.7 []. finally, the newick formula was uploaded in njplot 2.3 (http://doua.prabi.fr/software/njplot) [] to visualize and root the corresponding phylogenetic tree using s. oralis uo5 as outgroup. this tree was named tree_9strains. a similar approach […]

2016
PMCID: 5095628
PMID: 27430258
DOI: 10.1292/jvms.16-0264

[…] per site were conducted using the clustal x program []. phylogenetic trees were generated by neighbor-joining method [] with 1,000 bootstraps using clustal x program and then visualized with njplot []. the nucleotide sequence data reported in this study have been deposited in the ddbj database under the accession number lc041132. whole genome sequences of other apmvs for comparison […]


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NJplot in publications

 (126)
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 […]

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 […]

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 […]

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’ […]

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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