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Geneious specifications


Unique identifier OMICS_00016
Name Geneious
Alternative names Geneious Basic, genieous
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


No version available



  • person_outline Peter Meintjes

Publication for Geneious

Geneious citations


Bat Caliciviruses and Human Noroviruses Are Antigenically Similar and Have Overlapping Histo Blood Group Antigen Binding Profiles

PMCID: 5964351
DOI: 10.1128/mBio.00869-18
call_split See protocol

[…] colored bat) using the sequence-independent single-primer amplification technique and 454 next-generation sequencing platform. De novo contigs were assembled using three programs: Codon Code Aligner, Geneious, and DNAStar. Viral amino acid sequences were created using Vector NTI. Assembled contigs were analyzed using the basic local alignment search tool (BLAST) from the National Center for Biotec […]


Genetic diversity of PRRSV 1 in Central Eastern Europe in 1994–2014: origin and evolution of the virus in the region

Sci Rep
PMCID: 5958080
PMID: 29773820
DOI: 10.1038/s41598-018-26036-w
call_split See protocol

[…] type 1 representing the full range of genetic diversity of this Subtype. Altogether 607 sequences were analyzed in the study (Supplementary Table). Sequence alignment was performed based on ClustalW (Geneious 10.1.3, Biomatters) and phylogenetic analysis using a Bayesian Markov chain Monte Carlo method in MrBayes v3.2. Detailed parameter settings and the principles of lineage definitions were iden […]


An epizootic of Chlamydia psittaci equine reproductive loss associated with suspected spillover from native Australian parrots

PMCID: 5953950
PMID: 29765033
DOI: 10.1038/s41426-018-0089-y

[…] e covered. De novo assembled contigs for each sample were analysed in discontiguous BLAST to identify chlamydial contigs and contaminating DNA. Contig ordering and manual curation was conducted using Geneious mapper with high sensitivity and up to five times iteration in Geneious 10 workbench, following automated annotation of draft genomes in RAST. Genomes are deposited in Genbank under CP025423- […]


Chitinase genes (CHIAs) provide genomic footprints of a post Cretaceous dietary radiation in placental mammals

Sci Adv
PMCID: 5955627
PMID: 29774238
DOI: 10.1126/sciadv.aar6478

[…] aetophractus vellerosus, and Tolypeutes matacus; and made available to us by the Broad Institute. The latter assemblies were imported into Geneious v. 9.1.8 () for analysis. For annotated gene models, we obtained sequences derived from NCBI’s Eukaryotic Genome Annotation (EGA) pipeline by BLASTing (discontiguous megablast) a human CHIA m […]


Endocytosis mediated siderophore uptake as a strategy for Fe acquisition in diatoms

Sci Adv
PMCID: 5955625
PMID: 29774236
DOI: 10.1126/sciadv.aar4536
call_split See protocol

[…] by a BLASTp best hit against version 3 of the P. tricornutum genome (). The resulting set of sequences was aligned using the first 20× iterations of MAFFT v8 and then the inbuilt alignment builder in Geneious v.4.76 under the default criteria. Where multiple sequences were retrieved for individual species, a species consensus was generated. Only 36 species were found to contain ISIP1, of which 28 […]


High species diversity of trichostrongyle parasite communities within and between Western Canadian commercial and conservation bison herds revealed by nemabiome metabarcoding

PMCID: 5952520
PMID: 29764472
DOI: 10.1186/s13071-018-2880-y

[…] ncluded in the analysis were created. A list of all sequences and accession numbers used are provided in Additional file : FASTA Database. For each species, all available sequences were aligned using Geneious (version 10.1.3 (created by Biomatters), available from, using the MUSCLE algorithm with default parameters. A consensus sequence was generated for each species, from ea […]


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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.