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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.
Distributed Evolutionary Algorithms in Python (DEAP) is an evolutionary computation framework for rapid prototyping and testing of ideas. [2] [3] [4] It incorporates the data structures and tools required to implement most common evolutionary computation techniques such as genetic algorithm, genetic programming, evolution strategies, particle swarm optimization, differential evolution, traffic ...
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.
Salmon is a software tool for computing transcript abundance from RNA-seq data using either an alignment-free (based directly on the raw reads) or an alignment-based (based on pre-computed alignments) approach. It uses an online stochastic optimization approach to maximize the likelihood of the transcript abundances under the observed data.
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.
Waikato Environment for Knowledge Analysis (Weka) is a collection of machine learning and data analysis free software licensed under the GNU General Public License.It was developed at the University of Waikato, New Zealand and is the companion software to the book "Data Mining: Practical Machine Learning Tools and Techniques".
Spyder is extensible with first-party and third-party plugins, [8] and includes support for interactive tools for data inspection and embeds Python-specific code quality assurance and introspection instruments, such as Pyflakes, Pylint [9] and Rope. [10] [11] Spyder uses Qt for its GUI and is designed to use either of the PyQt or PySide Python ...