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.

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

Supported Format Types

FormatExtensionsData TypesCommon Sources
Common Assembly Format*.cafContigsSequencher
Clone Manager*.cm5Nucleotide sequencesClone Manager
CS FASTA*.csfastaColor spaceFASTA ABI SOLiD
DNAStar*.seq, *.pro, *.sbdNucleotide & protein sequencesDNAStar
DNA Strider*.strSequencesDNA Strider
Embl/UniProt*.embl, *.swpSequencesEmbl, UniProt
Endnote (8.0) XML*.xmlJournal article referencesEndnote, Journal article websites
Excel spreadsheet*.xlsx,*.xlsSpreadsheet filesMicrosoft Excel
FASTA*.fasta, *.fas, etc.Sequences, alignmentsPAUP*, ClustalX, BLAST, FASTA
FASTQ*.fastq, *.fasqSequences with qualitySolexa/Illumina
GenBank*.gb, *.xmlNucleotide & protein sequencesGenBank
Geneious*.xml, *.geneiousPreferences, databasesGeneious
GFF*.gffAnnotationsSanger Artemis
Molecular structure*.pdb, *.mol, *.xyz, *.cml, *.gpr, *.hin, *.nwo3D molecular structures3D structure databases and programs
Newick*.tre, *.tree, etc.Phylogenetic treesPHYLIP, Tree-Puzzle, PAUP*, ClustalX
Nexus*.nxs, *.nexTrees, AlignmentsPAUP*, Mesquite, MrBayes & MacClade
PDB*.pdb3D Protein structuresSP3, SP2, SPARKS, Protein Data Bank
PDF*.pdfDocuments, presentationsAdobe Writer, LATEX, Miktex
Phrap ACE*.aceContig assembliesPhrap/Consed
PileUp*.msfAlignments pileup(gcg)
PIR/NBRF*.pirSequences, alignmentsNBRF PIR
Qual*.qualQuality fileAssociated with a FASTA file
Raw sequence text*.seqSequencesAny file that contains only a sequence,
Rich Sequence Format*.rsfSequences, alignmentsGCGs NetFetch
Comma/Tab Separated Values*.csv, *.tsvSpreadsheet filesMicrosoft Excel
SAM/BAM*.sam, *.bamContigsSAMtools
Sequence Chromatograms*.ab1, *.scfRaw sequencing trace & sequenceSequencing machines
SnapGene*.dna, *.protSequences, annotations, metadataSnapGene
Variant Call Format*.vcfVariant calls/SNPsVariant callers and databases
Vector NTI sequence*.gb, *.gpNucleotide & protein sequencesVector NTI
Vector NTI/AlignX alignment*.aprAlignmentsVector NTI, AlignX
Vector NTI Archive*.ma4, *.pa4, *.oa4, *.ea4, *.ca6Nucleotide & protein sequences, enzyme sets and publicationsVector NTI
Vector NTI/ContigExpress*.cepNucleotide sequence assembliesVector NTI
Vector NTI databaseVNTI DatabaseNucleotide & protein sequences, enzyme sets and publicationsVector NTI

Export Format Options

Any set of documents may be exported in Geneious native format.

Data TypeFormat
DNA sequenceFASTA, Genbank XML, Genbank flat, Geneious
Amino acid sequenceFASTA, Genbank XML, Genbank flat, Geneious
Chromatogram sequenceABI, Geneious
Sequence with qualityFastQ, Qual, Geneious
AnnotationGFF, BED, VCF, Geneious
Multiple sequence alignmentPhylip, FASTA, NEXUS, MEGA3, Geneious
AssemblyPhrap ACE, Geneious, SAM/BAM, Geneious
Phylogenetic treePhylip, FASTA, NEXUS, Newick, MEGA3, Geneious
PDF documentPDF, Geneious
PublicationEndNote 8.0, Geneious
GraphsCSV or WIG, or images




Assembly and Mapping

De novo assembly or reference mapping using industry leading algorithms, including TopHat and Velvet.

Sanger Sequencing

Trim, assemble, and view Sanger sequencing trace files. Powerful SNP detection and variant calling.

Searching and NCBI

Rapidly search all key databases at NCBI for literature, DNA and protein sequence information.

Vector NTI Database Importer

Simple drag and drop of Vector NTI databases into Geneious Prime


Quick Start to Geneious Prime
How to perform Sanger Sequencing
How to work with GenBank
How to perform BLAST searching
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.  
Dr. Paula WelanderBroad Institute of MIT and Harvard