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
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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

Explore Geneious Prime

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.

Geneious Cloud

All of your data and notes saved and accessible in a secure, cloud workspace

Geneious Academy

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