Geneious pipeline

Geneious specifications


Unique identifier OMICS_00016
Name Geneious
Alternative name Geneious Basic
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License Commercial
Computer skills Medium
Version 11.1.4
Stability Stable
Free trial Yes
Maintained Yes


  • EMBOSS:dotmatcher


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  • person_outline Peter Meintjes <>

Publication for Geneious

Geneious IN pipelines

PMCID: 5722268
PMID: 29236931
DOI: 10.1590/0074-02760170119

[…] whole-genome sequencing was performed through illumina™ miseq platform with 300 bp paired-end library. de novo assembly was performed with clc genomics workbench 7.5.1 (clc bio, denmark) and geneious 10.0.3 (biomatters ltd, auckland, new zealand)., the obtained contigs were ordered according to l. interrogans serovar copenhageni strain fiocruz l1-130 reference genome (genbank accession […]

PMCID: 5750389
PMID: 29299531
DOI: 10.1128/mSphereDirect.00463-17

[…] (aaa46455.1)., the above-mentioned nucleotide or protein sequences were aligned with multiple alignment using fast fourier transform (mafft; within the geneious 10 software package (biomatters, auckland, new zealand). for each coronavirus species, s protein sequence alignments enabled us to determine the demarcation between s1 and s2 domains based […]

PMCID: 5751821
PMID: 29295716
DOI: 10.1186/s13071-017-2577-7

[…] (bigdye terminator v.3.1 chemistry, applied biosystems, foster city, ca, usa) using primers msp-3 and msp-4b in separate reactions. its sequences were aligned and analysed using the program geneious v.10 [60] and compared with sequences from the genbank database (additional file 1: table s1). enterocytozoon bieneusi sequence types or genotypes were named according to a recent […]

PMCID: 5764372
PMID: 29324824
DOI: 10.1371/journal.pone.0191183

[…] on an abi 3130 (life technologies, carlsbad, ca, usa) capillary sequencer following standard protocols. sequence chromatograms were assembled into contigs, edited, and aligned using clustalw in geneious 8.1.7 (biomatters inc., auckland, new zealand). gene alignments were exported as fasta files for subsequent analyses. sequences are deposited in genbank under accession numbers […]

PMCID: 5771137
PMID: 29338683
DOI: 10.1186/s12864-017-4429-4

[…] detection for the algorithm; a scoring matrix of 200 pam/k = 2; a gap opening penalty of 1.53; and an offset value of 0.123. a consensus sequence was then created for each species using the default geneious settings. finally, a phylogenetic tree was constructed using the phyml plug-in [51]. the tree was based on an hky85 substitution model [52] and features 100-bootstrap branch support; […]

Geneious institution(s)
Biomatters Ltd., Auckland, New Zealand; School of Agriculture and Food Science, University of Queensland, Brisbane, QLD, Australia; Department of Computer Science, University of Auckland, Auckland, New Zealand

Geneious review

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Erica Souza

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Geneious is a friendly tools, specially for who never work with any genetic analysis. The software have an intuitive graphic interface and you can do a simple analyze like gene alignment and a modern analysis like a de novo alignment. Also, the software are interconnected with NCBI and you can use BLASTn (for example) without exit the software.