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Citations per year

Number of citations per year for the bioinformatics software tool Primaclade

Tool usage distribution map

This map represents all the scientific publications referring to Primaclade per scientific context
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Primaclade specifications


Unique identifier OMICS_02356
Name Primaclade
Interface Web user interface
Restrictions to use None
Input format FASTA, clustalw, PHYLIP, nexus, mega, emboss
Output data A page containing the original alignment file displayed horizontally across the top of the page, followed by a single line showing the consensus sequence, the list of generated primers corresponding to their correct position within the alignment display and reverse complement for the 3' primers.
Output format HTML
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Elizabeth A. Kellogg


Unique identifier OMICS_02356
Name Primaclade
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Comprehensive Perl Archive Network (CPAN) Perl modules, BioPerl modules, the Primer3 software


No version available


This tool is not maintained anymore.

Publication for Primaclade

Primaclade citations


Genetic Analysis of Human Norovirus Strains in Japan in 2016–2017

Front Microbiol
PMCID: 5778136
PMID: 29403456
DOI: 10.3389/fmicb.2018.00001

[…] PCR) was performed using a PrimeScript II High Fidelity One Step RT-PCR Kit (TaKaRa). Using primer walking methods, we analyzed the complete RdRp region and VP1 gene. The primers were designed by the PrimaClade server (Supplementary Table ) (). After the PCR products were purified using a MinElute PCR Purification Kit (Qiagen), they were sequenced using a BigDye Terminator v3.1 Cycle Sequencing ki […]


Phylogeny and Immunoreactivity of Norovirus GII.P16 GII.2, Japan, Winter 2016–17

PMCID: 5749477
PMID: 29260675
DOI: 10.3201/eid2401.170284

[…] . 576). We performed viral RNA extraction and reverse transcription PCRs as described (). To analyze the complete RdRp region and VP1 gene, we used primer-walking methods with primers designed by the PrimaClade server ( Table 1) () and performed sequencing as described (). To determine the genotype of the current virus, we used Norovirus Genotyping Tool version 1.0 (). The accession numbers of the […]


Genetic Correlates of Individual Differences in Sleep Behavior of Free Living Great Tits (Parus major)

PMCID: 4777123
PMID: 26739645
DOI: 10.1534/g3.115.024216

[…] peats (see File S1 for PCR details, and Table S2 for primer details) based on the zebra finch sequence and an aligned sequence from a second bird species (either chicken or medium ground finch) using PrimaClade (). Primers were between 19 and 24 bases long, with one or two degenerate positions if necessary. We were able to design primers that functioned in great tits for 11 candidate genes. Once w […]


Cold Treatment Breaks Dormancy but Jeopardizes Flower Quality in Camellia japonica L.

Front Plant Sci
PMCID: 4641915
PMID: 26617623
DOI: 10.3389/fpls.2015.00983
call_split See protocol

[…] A set of primers was designed for five dormancy-related and four flower color-related target genes (Table ) using the web-based software Primaclade (The Kellogg Lab, University of Missouri), basing on multiple alignments of sequences lodged in GenBank belonging to C. sinensis and phylogenetically related species. Primer quality check f […]


Application of the Phylogenetic Species Concept to Wallemia sebi from House Dust and Indoor Air Revealed by Multi Locus Genealogical Concordance

PLoS One
PMCID: 4370657
PMID: 25799362
DOI: 10.1371/journal.pone.0120894

[…] Wallemia sebi specific primers were designed using PrimaClade [] for RPB1 and RPB2 genes from MAFFT v7.122b [] alignment of existing Wallemia sequences []. Wallemia sebi specific primers for MCM7 and TSR1 genes were designed from the genome annotation […]


Comparative and Evolutionary Analyses of Meloidogyne spp. Based on Mitochondrial Genome Sequences

PLoS One
PMCID: 4370701
PMID: 25799071
DOI: 10.1371/journal.pone.0121142

[…] ing primers: Mmt5 (5`-GGTTTAATTGGTGGTTTTGG-3`), Mmt2rc (5`-TGTCCTCAAACTAAACAACC-3`), Mmt9 (5`-TTGGTTGATTGGTGAAAGC-3`), and Mmt4rc (5`-AAACCACCAATTAAACCAGG-3`). Primers were designed with the software Primaclade [] based on a sequence alignment of available Meloidogyne species. PCR conditions included an initial denaturing step at 94°C for 2 min, followed by 35 cycles of 94°C for 30 seconds, 45°C f […]

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Primaclade institution(s)
Department of Biology, University of Missouri-St Louis, One University Boulevard, St Louis, MO, USA
Primaclade funding source(s)
Supported by NSF grants MCB-0110809 and DBI-0110189.

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