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

Format Extensions Data Types Common Sources
BED *.bed Annotations UCSC
Common Assembly Format *.caf Contigs Sequencher
Clone Manager *.cm5 Nucleotide sequences Clone Manager
Clustal *.aln Alignments ClustalX
CS FASTA *.csfasta Color space FASTA ABI SOLiD
DNAStar *.seq, *.pro, *.sbd 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
GCG *.seq Sequences GCG,
GenBank *.gb, *.xml Nucleotide & protein sequences GenBank
Geneious *.xml, *.geneious Preferences, databases Geneious
GFF *.gff Annotations Sanger Artemis
MEGA *.meg Alignments MEGA
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
PDF *.pdf Documents, presentations Adobe Writer, LATEX, Miktex
Phrap ACE *.ace Contig assemblies Phrap/Consed
PileUp *.msf Alignments pileup (gcg)
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
SAM/BAM *.sam, *.bam Contigs SAMtools
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.

Data Type 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




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