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 3.3-3
Stability Stable
Source code URL https://cran.r-project.org/src/contrib/seqinr_3.4-5.tar.gz
Maintained Yes

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Maintainer


  • person_outline Simon Penel <>

seqinr citations

 (3)
2015
PMCID: 4776708

[…] codon alignment, using a homemade python script. codon alignments were finally manually checked using aliview (larsson 2014)., the ds was calculated using the method of li (1993) implemented in the seqinr package (charif and lobry 2007), with a pairwise deletion option. the cub was estimated for host genes and tes as the enc according to wright’s method (wright 1990). the enc varies from 20 […]

2013
PMCID: 3840698

[…] removed using cd-hit (swindell, 46) with the parameters −c 0.99 –n 5, that is, a 99% sequence identity cut-off and a word size of 5. finally, cds sequence sets were filtered using functions in the seqinr package (charif & lobry, 4) in r (r development core team, 35) to only contain proteins that start with a start codon (m), with a minimum length of 30 amino acids (aa), only containing […]

2011
PMCID: 3163468

[…] products of the tested strain with the c58 genome (supplementary table s3, supplementary material online)., effective counts of the 64 codons of the 5,355 cdss of c58 were calculated using the “seqinr” package from r project (charif and lobry 2007). correspondence analyses were performed and projected using “dudi.coa” and “s.class” functions from the “ade4” package (dufour and dray 2007)., […]

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