Geneious Prime

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

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.

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
Export and submit to GenBank
Share files and folders with your team with Geneious Cloud

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