seqinr pipeline

seqinr specifications


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
Maintained Yes



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  • person_outline Simon Penel <>

seqinr citations

PMCID: 5296313

[…] the sequences of all the strains belonging to the same species. for those species with only a single strain, the concatenated sequence was used. the consensus dna sequences were obtained using the r seqinr package (charif and lobry, 2007) and the majority method option, in which the character with the highest frequency is returned as the consensus character. in the second approach, we generated […]

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 […]

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