seqinr protocols

View seqinr computational protocol

seqinr statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Dot plot generation chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

seqinr specifications

Information


Unique identifier OMICS_15909
Name seqinr
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 3.4-5
Stability Stable
Requirements
ade4, R(≥2.10.0), segmented
Source code URL https://cran.r-project.org/src/contrib/seqinr_3.4-5.tar.gz
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Simon Penel <>

seqinr in pipelines

 (18)
2018
PMCID: 5772385
PMID: 29362695
DOI: 10.7717/peerj.4261

[…]  top blastp hit). gene targets were selected based on annotations related to gene regulation, immune response, and growth (). corresponding contigs were then selected from the transcriptome using the seqinr package (). ncbi primer blast was used to develop primers for qpcr using the following parameters: amplicon size 100–400 bp, gc content 55–60%, melt temperatures ∼60 °c and within 0.5 °c of eac […]

2018
PMCID: 5786225
PMID: 29325123
DOI: 10.1093/gbe/evy005

[…] case dsgta coverage) peaks, indicating periodicity of the data. cumulative gc/at-skew for identification of the origin and terminus of replication has been performed using the oriloc function of the seqinr package ()., linux shell and r scripts for analysis are available at https://github.com/juergent79/gta; last accessed january 15, 2018., the tool phast () was used to identify phage derived […]

2018
PMCID: 5890265
PMID: 29632298
DOI: 10.1038/s41467-018-03724-9

[…] alignment. furthermore, we only used transposable elements were both dnmt and reverse transcriptase domains passed the quality filters. finally, we obtained the ka, ks and ka/ks values using the 'seqinr' package for r in cran. for interspecies comparisons, we preselected candidate sequences from all lineages depicted in fig.  and used tblastn to obtain the best hit in each of the four […]

2018
PMCID: 5942634
PMID: 29768530
DOI: 10.1590/0074-02760170385

[…] correction, were removed of selection and phylodynamic analyses., codon preferences analyses - we employed the relative synonymous codon usage method with the r-package seqin{r} v3.13 (http://seqinr.r-forge.r-project.org/) to estimate the codon preferences for each polyprotein gene sequence. in addition, we employed a principal component analysis (pca) to assess patterns among relative […]

2017
PMCID: 5234253
PMID: 28086780
DOI: 10.1186/s12864-016-3443-2

[…] was analysed using the jalview software [] and processed using the mrbayes [, ], a bayesian markov chain monte carlo (mcmc) package for phylogenetic analysis. the functions made available in the seqinr and ape r packages [] were used to convert the multiple alignment in fasta format into a nexus file required as input by mrbayes. metropolis coupling of the mcmc sampling of the target […]


To access a full list of citations, you will need to upgrade to our premium service.

seqinr in publications

 (123)
PMCID: 5954121
PMID: 29765018
DOI: 10.1038/s41467-018-04217-5

[…] for public use on the lanl hiv database (www.hiv.lanl.gov/content/sequence/rap2017/rap.html). all software is developed in c++, r, and cgi. the r code utilizes functions from the packages ape and seqinr., to determine the impact of recombination on the emergence of antibody resistance, we ran rapr on 341 env sequences from ch0505, spanning day 19 through day 692 since infection. of these, 123 […]

PMCID: 5942634
PMID: 29768530
DOI: 10.1590/0074-02760170385

[…] correction, were removed of selection and phylodynamic analyses., codon preferences analyses - we employed the relative synonymous codon usage method with the r-package seqin{r} v3.13 (http://seqinr.r-forge.r-project.org/) to estimate the codon preferences for each polyprotein gene sequence. in addition, we employed a principal component analysis (pca) to assess patterns among relative […]

PMCID: 5890265
PMID: 29632298
DOI: 10.1038/s41467-018-03724-9

[…] alignment. furthermore, we only used transposable elements were both dnmt and reverse transcriptase domains passed the quality filters. finally, we obtained the ka, ks and ka/ks values using the 'seqinr' package for r in cran. for interspecies comparisons, we preselected candidate sequences from all lineages depicted in fig.  and used tblastn to obtain the best hit in each of the four […]

PMCID: 5924522
PMID: 29587435
DOI: 10.3390/genes9040180

[…] de novo using trinity and a k-mer length of 25 from all reads (both strains and all time points) []. the longest transcript for each component were retained using custom scripts and the r package seqinr []. this transcriptome is available in dryad (doi:10.5061/dryad.k7t20)., the set of longest transcripts was indexed as a reference transcriptome, and the individual reads were mapped back […]

PMCID: 5823862
PMID: 29472617
DOI: 10.1038/s41598-018-21645-x

[…] doubling the median value in windows of 1000 bp (shift of 100 bp)., genomic gc content was calculated in the same 1000 bp sliding windows mentioned above, using the gc function of the r package seqinr., the samples were tested for inherited hhv-6 integration presence using digital droplet pcr (ddpcr). the experiments followed the method proposed by sedlack et al., starting from 150 ng […]


To access a full list of publications, you will need to upgrade to our premium service.

seqinr reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review seqinr