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Nextstrain is a collaboration between researchers in Seattle, United States [1] and Basel, Switzerland [2] which provides a collection of open-source tools for visualising the genetics behind the spread of viral outbreaks.
A user with a full genome sequence of a sample of SARS-CoV-2 can use the tool to submit that sequence, which is then compared with other genome sequences, and assigned the most likely lineage (Pango lineage). [5] Single or multiple runs are possible, and the tool can return further information regarding the known history of the assigned lineage ...
The Biopython project is an open-source collection of non-commercial Python tools for computational biology and bioinformatics, created by an international association of developers. [ 1 ] [ 4 ] [ 5 ] It contains classes to represent biological sequences and sequence annotations , and it is able to read and write to a variety of file formats.
PHYLogeny Inference Package (PHYLIP) is a free computational phylogenetics package of programs for inferring evolutionary trees (phylogenies). [1] It consists of 65 portable programs, i.e., the source code is written in the programming language C.
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.
KNIME (/ n aɪ m / ⓘ), the Konstanz Information Miner, [2] is a free and open-source data analytics, reporting and integration platform.KNIME integrates various components for machine learning and data mining through its modular data pipelining "Building Blocks of Analytics" concept.
New python bindings with supports for several builtins, matrix operations, federated tensors and lineage traces. Cuda implementation of cumulative aggregate operators (cumsum, cumprod etc.) New model debugging technique with slice finder. New tensor data model (basic tensors of different value types, data tensors with schema) [experimental]
Data lineage can be visualized at various levels based on the granularity of the view. At a very high-level, data lineage is visualized as systems that the data interacts with before it reaches its destination. At its most granular, visualizations at the data point level can provide the details of the data point and its historical behavior ...