Editing List of file formats (section)

=== Biology ===
Molecular biology and bioinformatics:
* AB1 – In [[DNA sequencing]], [[chromatogram]] files used by instruments from [[Applied Biosystems]]
* ACE – A [[sequence assembly]] format
* ASN.1 – [[Abstract Syntax Notation One]], is an International Standards Organization ([[International Organization for Standardization|ISO]]) data representation format used to achieve interoperability between platforms. [[National Center for Biotechnology Information|NCBI]] uses ASN.1 for the storage and retrieval of data such as nucleotide and protein sequences, structures, genomes, and PubMed records.
* BAM – [[Binary Alignment/Map]] format (compressed SAM format)
* BCF – Binary compressed VCF format
* BED – The [[BED file format|browser extensible display format]] is used for describing [[gene]]s and other features of [[DNA]] sequences
* CAF – Common Assembly Format for [[sequence assembly]]
* [[CRAM (file format)|CRAM]] – compressed file format for storing biological sequences aligned to a reference sequence
* DDBJ – The flatfile format used by the [[DNA Data Bank of Japan|DDBJ]] to represent database records for [[nucleotide sequence|nucleotide]] and [[peptide sequence]]s from [[DDBJ]] databases.
* EMBL – The flatfile format used by the [[European Molecular Biology Laboratory|EMBL]] to represent database records for [[nucleotide sequence|nucleotide]] and [[peptide sequence]]s from [[EMBL]] databases.
* FASTA – The [[FASTA format]], for sequence data. Sometimes also given as FNA or FAA (Fasta Nucleic Acid or Fasta Amino Acid).
* FASTQ – The [[FASTQ format]], for sequence data with quality. Sometimes also given as QUAL.
* GCPROJ – The [[Genome Compiler]] project. Advanced format for genetic data to be designed, shared and visualized.
* GenBank – The flatfile format used by the [[National Center for Biotechnology Information|NCBI]] to represent database records for [[nucleotide sequence|nucleotide]] and [[peptide sequence]]s from the [[GenBank]] and [[RefSeq]] databases
* GFF – The [[General feature format]] is used to describe [[gene]]s and other features of [[DNA]], [[RNA]], and [[protein]] sequences
* GTF – The [[Gene transfer format]] is used to hold information about [[gene]] structure
* MAF – The [[Multiple Alignment Format]] stores multiple alignments for whole-genome to whole-genome comparisons [https://biopython.org/wiki/Multiple_Alignment_Format]
* NCBI – Structured [[ASN.1]] format used at [[National Center for Biotechnology Information]] for DNA and protein data
* NEXUS – The [[Nexus file]] encodes mixed information about genetic sequence data in a block structured format
* NeXML – XML format for [[phylogenetic tree]]s
* NWK – The [[Newick format|Newick tree format]] is a way of representing graph-theoretical trees with edge lengths using parentheses and commas and useful to hold [[phylogenetic tree]]s.
* PDB – structures of biomolecules deposited in [[Protein Data Bank]], also used to exchange protein and nucleic acid structures
* PHD – Phred output, from the base-calling software [[Phred (software)|Phred]]
* PLN – Protein Line Notation used in [http://www.biochemfusion.com/products/ proteax software] [http://www.biochemfusion.com/doc/Biochemfusion_PLN_1.4_spec.pdf specification]
* SAM – [[SAM (file format)|SAM]], Sequence Alignment Map format, in which the results of the [[1000 Genomes Project]] will be released
* SBML – [[SBML|The Systems Biology Markup Language]] is used to store biochemical network computational models
* SCF – Staden chromatogram files used to store data from [[DNA sequencing]]
* SFF – [[Standard Flowgram Format]]
* SRA – format used by the [[National Center for Biotechnology Information]] Short Read Archive to store high-throughput DNA sequence data
* Stockholm – The [[Stockholm format]] for representing [[multiple sequence alignment]]s
* Swiss-Prot – The flatfile format used to represent database records for [[peptide sequence|protein]] sequences from the [[Swiss-Prot]] database
* VCF – [[Variant Call Format]], a standard created by the [[1000 Genomes Project]] that lists and annotates the entire collection of human variants (with the exception of approximately 1.6 million variants).