Import and export sequence data

Share your data. Import, export and convert common file types as well as their annotations and notes.

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 a whole lot of data from everywhere? Upgrading to Geneious is easy with a simple drag and drop import of a vast range of formats.

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
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 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
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 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