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MNHN-Tree-Tools: MNHN-Tree-Tools is an opensource phylogenetics inference software working on nucleic and protein sequences. Clustering of DNA or protein sequences and phylogenetic tree inference from a set of sequences. At the core it employs a distance-density based approach. Thomas Haschka, Loïc Ponger, Christophe Escudé and Julien ...
Enriched data lineage may include additional elements such as data quality test results, reference data, data models, business terminology, data stewardship information, program management details and enterprise systems associated with data points and transformations. Data lineage visualization tools often include masking features that allow ...
Distinct from the PANGOLIN tool, Pango lineages are regularly, manually curated based on the current globally circulating diversity. A large phylogenetic tree is constructed from an alignment containing publicly available SARS-CoV-2 genomes, and sub-clusters of sequences in this tree are manually examined and cross-referenced against epidemiological information to designate new lineages; these ...
Phylogenetic trees generated by computational phylogenetics can be either rooted or unrooted depending on the input data and the algorithm used. A rooted tree is a directed graph that explicitly identifies a most recent common ancestor (MRCA), [citation needed] usually an inputed sequence that is not represented in the input.
The Smith-Waterman algorithm was an extension of a previous optimal method, the Needleman–Wunsch algorithm, which was the first sequence alignment algorithm that was guaranteed to find the best possible alignment. However, the time and space requirements of these optimal algorithms far exceed the requirements of BLAST.
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The toolkit comprises user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. It also includes few other tools, which are helpful in NGS data quality control and analysis.
A term closely related to data archaeology is data lineage. The first step in performing data archaeology is an investigation into their data lineage. Data lineage entails the history of the data, its source and any alterations or transformations they have undergone. Data lineage can be found in the metadata of a dataset, the para data of a ...