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The extensible NEXUS file format is widely used in bioinformatics.It stores information about taxa, morphological and molecular characters, distances, genetic codes, assumptions, sets, trees, etc. [1] Several popular phylogenetic programs such as PAUP*, [2] MrBayes, [3] Mesquite, [4] MacClade [5] and SplitsTree [6] use this format.
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This allows a sequence that was obtained from a database to be labelled with a reference to its database record. The database identifier format is understood by the NCBI tools like makeblastdb and table2asn. The following list describes the NCBI FASTA defined format for sequence identifiers. [9]
The NCBI assigns a unique identifier (taxonomy ID number) to each species of organism. [5] The NCBI has software tools that are available through web browsers or by FTP. For example, BLAST is a sequence similarity searching program. BLAST can do sequence comparisons against the GenBank DNA database in less than 15 seconds.
Note that more recent versions of Illumina software output a sample number (defined by the order of the samples in the sample sheet) in place of an index sequence when an index sequence is not explicitly specified for a sample in the sample sheet. For example, the following header might appear in a FASTQ file belonging to the first sample of a ...
Many of these templates can create anchors that allow links from reference templates that are placed in-text with the content to the full citation in the reference list. These links are a convenience and are not a requirement; the use of reference and citation templates is also not required.
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part of the National Institutes of Health in the United States) as part of the International Nucleotide Sequence Database Collaboration (INSDC).
Template is used to navigate through a sequence of articles. Template parameters [Edit template data] This template prefers block formatting of parameters. Parameter Description Type Status Previous prev The previous page in the series, can be wiki-linked. Default — Example [[Timeline of United States history (1860–1899)|1860–1899]] String suggested List list The title of the series, can ...