Organize, search and share sequence databases
Arrange and browse your data library how you like.
- Add and remove sequence databases
- Document history automatically saved
- Batch export
- Batch rename
- Filter documents based on fields
- Share annotated sequence files
- Export and submit to Genbank
Wide ranging file format compatibility from FASTA to VectorNTI
Have data from multiple sources, including different sequencing machines and other sequence analysis software? Loading into Geneious Prime is easy with a simple drag and drop import of a vast range of formats.
Dedicated importer for Vector NTI Express and Advance databases preserves metadata, full database structure including subsets, and lineage information.
Smart NGS File Importing
Drop any assortment of SAM, BAM, GFF, BED, and VCF files into Geneious to import in one easy step, even if you have a mixture of different samples and reference sequences.
Supported Format Types
|Format||Extensions||Data Types||Common Sources|
|Common Assembly Format||*.caf||Contigs||Sequencher|
|Clone Manager||*.cm5||Nucleotide sequences||Clone Manager|
|CS FASTA||*.csfasta||Color space||FASTA ABI SOLiD|
|DNAStar||*.seq, *.pro||Nucleotide & protein sequences||DNAStar|
|DNA Strider||*.str||Sequences||DNA Strider|
|Embl/UniProt||*.embl, *.swp||Sequences||Embl, UniProt|
|Endnote (8.0) XML||*.xml||Journal article references||Endnote, Journal article websites|
|FASTA||*.fasta, *.fas, etc.||Sequences, alignments||PAUP*, ClustalX, BLAST, FASTA|
|FASTQ||*.fastq, *.fasq||Sequences with quality||Solexa/Illumina|
|GenBank||*.gb, *.xml||Nucleotide & protein sequences||GenBank|
|Geneious||*.xml, *.geneious||Preferences, databases||Geneious|
|Molecular structure||*.pdb, *.mol, *.xyz, *.cml, *.gpr, *.hin, *.nwo||3D molecular structures||3D structure databases and programs|
|Newick||*.tre, *.tree, etc.||Phylogenetic trees||PHYLIP, Tree-Puzzle, PAUP*, ClustalX|
|Nexus||*.nxs, *.nex||Trees, Alignments||PAUP*, Mesquite, MrBayes & MacClade|
|PDB||*.pdb||3D Protein structures||SP3, SP2, SPARKS, Protein Data Bank|
|Documents, presentations||Adobe Writer, LATEX, Miktex|
|Phrap ACE||*.ace||Contig assemblies||Phrap/Consed|
|PIR/NBRF||*.pir||Sequences, alignments||NBRF PIR|
|Qual||*.qual||Quality ﬁle||Associated with a FASTA ﬁle|
|Raw sequence text||*.seq||Sequences||Any ﬁle that contains only a sequence,|
|Rich Sequence Format||*.rsf||Sequences, alignments||GCGs NetFetch|
|Comma/Tab Separated Values||*.csv, *.tsv||Spreadsheet ﬁles||Microsoft Excel|
|Sequence Chromatograms||*.ab1, *.scf||Raw sequencing trace & sequence||Sequencing machines|
|SnapGene||*.dna||Sequences, annotations, metadata||SnapGene|
|Variant Call Format||*.vcf||Variant calls/SNPs||Variant callers and databases|
|Vector NTI sequence||*.gb, *.gp||Nucleotide & protein sequences||Vector NTI|
|Vector NTI/AlignX alignment||*.apr||Alignments||Vector NTI, AlignX|
|Vector NTI Archive||*.ma4, *.pa4, *.oa4, *.ea4, *.ca6||Nucleotide & protein sequences, enzyme sets and publications||Vector NTI|
|Vector NTI/ContigExpress||*.cep||Nucleotide sequence assemblies||Vector NTI|
|Vector NTI database||VNTI Database||Nucleotide & protein sequences, enzyme sets and publications||Vector NTI|
Export Format Options
Any set of documents may be exported in Geneious native format.
|DNA sequence||FASTA, Genbank XML, Genbank ﬂat, Geneious|
|Amino acid sequence||FASTA, Genbank XML, Genbank ﬂat, Geneious|
|Chromatogram sequence||ABI, Geneious|
|Sequence with quality||FastQ, Qual, Geneious|
|Annotation||GFF, BED, VCF, Geneious|
|Multiple sequence alignment||Phylip, FASTA, NEXUS, MEGA3, Geneious|
|Assembly||Phrap ACE, Geneious, SAM/BAM, Geneious|
|Phylogenetic tree||Phylip, FASTA, NEXUS, Newick, MEGA3, Geneious|
|PDF document||PDF, Geneious|
|Publication||EndNote 8.0, Geneious|
|Graphs||CSV or WIG, or images|
More Geneious Prime Features
NGS Visualization and Analysis – Comprehensive analysis of data, including genome browser, contig visualization, SNP calling, and RNA-Seq expression analysis.
Alignment – Perform pairwise and multiple alignments of DNA or protein using trusted algorithms, including MAFFT and ClustalW.
Analysis and Annotation – Trim, assemble, annotate and view Sanger sequencing trace files
Molecular Cloning – View plasmid maps, automatically annotate vectors, find restriction sites; digest, ligate, and perform Golden Gate, Gibson, and Gateway cloning.
BLAST / NCBI – Connect to NCBI and PubMed, submit sequences directly to GenBank, BLAST sequences and search your own database.
I have found Geneious to be one of the most intuitive and powerful sequence analysis programs that I have used in all my years working in the molecular biology field. Thanks for making my life so much easier.
Geneious is an absolutely beautiful package to work with. We love it and we are telling everyone about it.
This program is wonderful! I was desperately looking for a software program that would make analyzing my sequencing data less painful. Thank you for developing a quality, user-friendly program. The interface is great!
Geneious is paramount in my research so I can’t be without it for too long.
The combination of powerful analytic features, intuitive navigation and file organization, and the responsiveness that representatives have shown to the inclusion of new functions has made us big fans of this software.
Geneious is a great software… I just want to express my appreciation to Biomatters to come up with such good product.
For many years I’ve wanted a friendly, menu-driven interface to our Glimmer program, but my research group has never had the resources available to build one. The Geneious Glimmer interface is terrific; it will allow any scientist to find genes in almost any bacterial, viral, or archaeal sequence, without requiring background expertise in Unix command-line programs. I’m also very pleased that Geneious makes Glimmer available across multiple computer platforms, including Windows and Mac.
We’ve been using our Geneious licenses a lot and really like the software. We’ve written several plug-ins ourselves and are using it more and more to analyze our data.
It’s not just about the buttons. From a user’s perspective, Phobos generates annotations, and Geneious handles annotations beautifully. The integration was obvious! And from a technical perspective it was easy to achieve, because it was simple to parse the outputs from Phobos into repeat annotations for the Geneious interface.
TopHat is a robust tool, but it was designed with experienced bioinformatics scientists in mind. Geneious makes TopHat accessible to many more users through the same powerful, intuitive user interface they have with other Geneious analysis tasks.