Geneious protocols

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Geneious statistics

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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


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  • person_outline Peter Meintjes <>

Publication for Geneious

Geneious in pipelines

PMCID: 5749474
PMID: 29260690
DOI: 10.3201/eid2401.171174

[…] independently. we performed sequence amplification and analysis for the random approach according to mee et al. () and for poliovirus-specific primers as described by stern et al. (). we used geneious r10 software ( for deep-sequencing data analysis. the nucleotide sequence of type 2 cvdpv isolate 2015-114-c6 has been deposited in genbank under accession no. […]

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 [] and compared with sequences from the genbank database (additional file : table s1). enterocytozoon bieneusi sequence types or genotypes were named according to a recent […]

PMCID: 5759284
PMID: 29310678
DOI: 10.1186/s12977-017-0383-0

[…] not contain signal peptide coding sequence., the following steps were performed during the meme and dnasp analysis. first, a multiple sequence alignment was generated using clustalw implemented in geneious pro 5.5.9 software (biomatters ltd). second, the aligned sequences were submitted to the meme server ( the meme analysis was run in zoops (zero or one per […]

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: 5770046
PMID: 29338017
DOI: 10.1371/journal.pone.0191042

[…] and identifying snps that were present in greater than 90% of reads at a depth of at least 10x. core snps were aligned and used to generate a maximum likelihood tree using the raxml wrapper in geneious r10 (biomatters, new zealand), using the gtr cat model and 100 bootstrap replicates []. sequences were de novo assembled into contigs using the spades v3.10.1 assembler []. contigs […]

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Geneious in publications

PMCID: 5964349
DOI: 10.1128/mBio.00809-18

[…] the right. (b) alignment of all c. crescentus hwe and hiska2 histidine kinases based on the presence of the highly conserved hrxxn motif in their dhp domains (). muscle alignments were performed in geneious v7.1.7 (biomatters ltd., auckland, new zealand). (c) autophosphorylation of nine c. crescentus hwe histidine kinases (upper panel) and phosphotransfer to mrra (lower panel). phosphorylation […]

PMCID: 5964351
DOI: 10.1128/mBio.00869-18

[…] 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 […]

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

[…] 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 […]

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

[…] 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 […]

PMCID: 5955625
PMID: 29774236
DOI: 10.1126/sciadv.aar4536

[…] 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 […]

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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.