NJplot pipeline

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 IN pipelines

 (19)
2017
PMCID: 5445277
PMID: 28545448
DOI: 10.1186/s12859-017-1696-7

[…] gene sequences were obtained from the kegg database on november 30, 2016. after multiple alignments of the nucleotide sequences using clustalw2 software, the phylogenetic tree was constructed using njplot (doua.prabi.fr/software/njplot). similar to our approach for logistic regression analyses, we constructed full models and then selected the best model based on aicc values. we also obtained […]

2017
PMCID: 5445277
PMID: 28545448
DOI: 10.1186/s12859-017-1696-7

[…] the kegg database on november 30, 2016. after multiple alignments of the nucleotide sequences using clustalw2 software, the phylogenetic tree was constructed using njplot (doua.prabi.fr/software/njplot). similar to our approach for logistic regression analyses, we constructed full models and then selected the best model based on aicc values. we also obtained the averaged models., […]

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

[…] by concatenated sequences using the neighbor-joining method [39]. clustal x software was used to align the sequences [40], and calculate the genetic distances. the dendrogram was constructed using njplot program [41] and mega 6 [42]., based on genomic analysis [27, 28], crispr loci are flanked by cas genes encoding cas proteins (fig 1). three cas genes (cas2, cas1 and cas9, in this order) […]

2017
PMCID: 5741697
PMID: 29326722
DOI: 10.3389/fimmu.2017.01855

[…] the sequences and clustalx2 for the sequence alignment. the maximum likelihood phylogenetic tree of the bacterial sequences was determined by using the web interface raxml black box3 (figure 1) and njplot to draw the phylogenetic tree4 (figure 1)., n-acyl homoserine lactone (ahl) production was measured as a surrogate for qs using the indicator strain chromobacterium violaceum (cv026), […]

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

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