Import and Export Sequence Data
Import, export and convert common file types as well as their annotations and notes with a simple drag and drop
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. Import files from any sequencing machine including Illumina, PacBio, Nanopore and Ion Torrent.
Dedicated importer for Vector NTI Express and Advance databases preserves metadata, full database structure including subsets, and lineage information.
Smart NGS file importing allows you to import any assortment of SAM, BAM, GFF, BED, and VCF files in one easy step, even if you have a mixture of different samples and reference sequences.
Import metadata onto sequences and other documents
Seamlessly attach new data from downstream analyses or other applications onto your sequences or update document fields, by importing columns from a CSV/TSV format spreadsheet onto documents that are already in Geneious Prime.
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|
|Excel spreadsheet||*.xlsx,*.xls||Spreadsheet files||Microsoft Excel|
|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, *.prot||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|
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I really like your program. I first got it to make alignment and trees of my sequences and it works well for those purposes. But it was a real lifesaver a few weeks ago when I lost my academic license to Vector NTI and couldn’t access any of my plasmids!! But I noticed I could import my database into Geneious and I was back in business.
Coming from the world of Vector NTI, I must tell you that Geneious looks and feel much better!