| File format | File extension | Read | Write | Comment |
|---|---|---|---|---|
| ABIF | *.ab1, *.abi, *.abif | + | - | A chromatogram file format. See also: Chromatogram Viewer |
| ACE | *.ace | + | - | A file format for storing data about genomic contigs. See also: Alignment Editor |
| APR | *.apr | + | - | Vector NTI / AlignX Alignment format. See also: Alignment Editor |
| Bairoch | *.bairoch | + | + | A file format to store enzymes. See also: Restriction Analysis |
| BAM | *.bam | + | - | Binary compressed SAM format. See also: Assembly Browser |
| ClustalW | *.aln | + | + | A multiple sequence alignments (MSA) file format. See also: Alignment Editor |
| EBWT | *.ebwt | + | + | A Bowtie prebuilt index file. See also: Bowtie |
| EMBL | *.em, *.emb, *.embl | + | - | A rich format for storing sequences and their annotations. See also: Sequence View |
| FASTA | *.fa, *.mpfa, *.fna, *.fsa, *.fas, *.fasta, *.sef *.seqs | + | + | One of the oldest and simplest sequence file format. See also: Sequence View |
| FASTQ | *.fastq | + | + | A file format used to store a sequence and its corresponding quality scores. It was originally developed at the “Wellcome Trust Sanger Institute”. See also: Sequence View |
| Genbank | *.gb, *.gbk, *.gen, *.genbank | + | + | A rich format for storing sequences and associated annotations. See also: Sequence View |
| GFF | *.gff | + | + | The Gene Finding Format (GFF) format is used to store features and annotations. See also: Sequence View |
| HMM | *.hmm | + | + | A file format to store HMM profiles. |
| MMDB | *.prt | + | - | ASN.1 format used by the Molecular Modeling Database (MMDB). See also: 3D Structure Viewer |
| MSF | *.msf | + | + | A multiple sequence alignments file format. See also: Alignment Editor |
| Mega | *.meg, *.meg.gz | + | A multiple sequence alignments file format. See also: Alignment Editor | |
| Newick | *.nwk, *.newick | + | + | A tree file format. See also: Building Phylogenetic Tree, Phylogenetic Tree Viewer |
| Nexus | *.nex *.nxs | + | + | A multiple alignment and phylogenetic trees file format. See also: Alignment Editor, Building Phylogenetic Tree, Phylogenetic Tree Viewer |
| PDB | *.pdb | + | - | The Protein Data Bank (PDB) format allows to view the 3D structure of the sequence. See also: 3D Structure Viewer |
| pDRAW32 | *.pdw | + | - | A sequence file format used by pDRAW32 software. See also: Sequence View |
| PFM | *.pfm | + | + | A file format for a position frequency matrix. See also: Weight Matrix |
| Phylip | *.phy | + | + | A multiple alignment file format. See also: Alignment Editor |
| PWM | *.pwm | + | + | A file format for a position weight matrix. See also: Weight Matrix |
| Raw | *.seq | + | + | A raw sequence format. See also: Sequence View |
| SAM | *.sam | + | + | The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences. See also: Assembly Browser, Bowtie, UGENE Genome Aligner |
| SCF | *.scf | + | - | It is a Standard Chromatogram Format. See also: Chromatogram Viewer |
| SITECON | *.sitecon | + | - | A file format to store TFBS profile. See also: SITECON |
| Stockholm | *.sto | + | + | A multiple sequence alignments file format. See also: Alignment Editor |
| Swiss-Prot | *.txt *.sw | + | - | An annotated protein sequence in format of the UniProtKB/Swiss-Prot database. See also: Sequence View |
| Vector NTI Sequence | *.gb *.gp | + | + | A rich format for storing sequences and associated annotations, produced by Vector NTI software. See also: Sequence View |
| VCF | *.vcf | + | + | The VCF specifies the format of a text file used for storing gene sequence variations. See also: Assembly Browser |
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