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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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Documentation


Maintainer


  • person_outline Simon Penel

seqinr citations

 (158)
library_books

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

2018
Nat Commun
PMCID: 5954121
PMID: 29765018
DOI: 10.1038/s41467-018-04217-5

[…] ble 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. […]

library_books

NS1 codon usage adaptation to humans in pandemic Zika virus

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

[…] nferroni 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 syn […]

library_books

Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons

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

[…] don 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 Symbiodi […]

library_books

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

2018
Genes
PMCID: 5924522
PMID: 29587435
DOI: 10.3390/genes9040180

[…] led 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). […]

library_books

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

2018
Sci Rep
PMCID: 5823862
PMID: 29472617
DOI: 10.1038/s41598-018-21645-x

[…] overage 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. […]

call_split

Effect of HIV/HCV Co Infection on the Protease Evolution of HIV 1B: A Pilot Study in a Pediatric Population

2018
Sci Rep
PMCID: 5799169
PMID: 29403002
DOI: 10.1038/s41598-018-19312-2
call_split See protocol

[…] een the mean number of non-synonymous (dN) and synonymous (dS) nucleotide substitutions per site (dN − dS) by Pamilo Bianchi method implemented in MEGA v7 and by Li-Wu-and-Luo method implemented in R SeqInr package. Since the two methods led to the same conclusions, only Pamilo-Bianchi results are shown. Individual values of dN and dS were also obtained. Tests for positive selection on individual […]

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