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Several online format converters exist to rapidly reformat multi-FASTA files to different formats (e.g. NEXUS, PHYLIP) for use with different phylogenetic programs, such as the converter available on phylogeny.fr. [26]
Compression of FASTA / UCSC2Bit files into random access compressed archives. Toolkit to mount FASTA files, indices and dictionary files virtually. This allows neat file system (api-like )integration without the need to fully decompress archives for random / partial access. FASTA files: Huffman coding as implemented by Zstd
The NEXUS format also allows the storage of data that can facilitate analyses, such as sets of characters or taxa. Many popular phylogenetic programs, including PAUP*, [2] MrBayes, [3] Mesquite, [4] MacClade, [5] and SplitsTree, [6] use this format. Nexus file names typically have the extension .nxs or .nex.
Input data can be in the three following formats: Newick format, PHYLIP and FASTA format. All graphical results provided by the T-REX server can be saved in the SVG (Scalable Vector Graphics) format and then opened and modified (e.g. prepared for a publication or presentation) in the user’s preferred graphics editor.
FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single ASCII character for brevity.
Biological sequence formats are a collection of file formats that are used in the biomedical sciences. There are a number of these. Most of these formats were developed for use in particular programmes and have subsequently been reused by other programmes. A number of web sites are available which will convert one of these formats to another.
FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. [1] Its legacy is the FASTA format which is now ubiquitous in bioinformatics .
Biopython can read and write to a number of common sequence formats, including FASTA, FASTQ, GenBank, Clustal, PHYLIP and NEXUS. When reading files, descriptive information in the file is used to populate the members of Biopython classes, such as SeqRecord. This allows records of one file format to be converted into others.