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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

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  • person_outline Simon Penel <>

seqinr citations

 (132)
library_books

Tracking HIV 1 recombination to resolve its contribution to HIV 1 evolution in natural infection

2018
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 […]

library_books

NS1 codon usage adaptation to humans in pandemic Zika virus

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 […]

library_books

Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons

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 […]

library_books

Non Pleiotropic Coupling of Daily and Seasonal Temporal Isolation in the European Corn Borer

2018
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 […]

library_books

Whole genome diversity of inherited chromosomally integrated HHV 6 derived from healthy individuals of diverse geographic origin

2018
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 […]

library_books

Positively Selected Effector Genes and Their Contribution to Virulence in the Smut Fungus Sporisorium reilianum

2018
PMCID: 5811872
PMID: 29390140
DOI: 10.1093/gbe/evy023

[…] similarities were computed in nonoverlapping windows of 10 kb., gene families with exactly one member in each species were concatenated and pairwise protein sequence similarities computed using the seqinr package for r (). protein alignments were also used to infer dates of divergence, using a relaxed clock model. the phylobayes version 4.1 software () was used with the auto-correlated model […]


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