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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.
The Molecular Modelling Toolkit (MMTK) is an open-source software package written in Python, which performs common tasks in molecular modelling.. The Molecular Modeling Toolkit is a library that implements common molecular simulation techniques, with an emphasis on biomolecular simulations.
Galaxy is open-source software implemented using the Python programming language. It is developed by the Galaxy team [23] at Penn State, Johns Hopkins University, Oregon Health & Science University, and the Galaxy Community. [24] Galaxy is extensible, as new command line tools can be integrated and shared within the Galaxy ToolShed. [25]
Open Bioinformatics Foundation: BioPerl: Perl language toolkit Cross-platform: Artistic, GPL: Open Bioinformatics Foundation: BioPHP: PHP language toolkit with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools Cross-platform: GPL v2 Open Bioinformatics Foundation: Biopython: Python ...
fastqp Simple FASTQ quality assessment using Python. Kraken: [9] A set of tools for quality control and analysis of high-throughput sequence data. HTSeq [10] The Python script htseq-qa takes a file with sequencing reads (either raw or aligned reads) and produces a PDF file with useful plots to assess the technical quality of a run.
Biskit is an open source software package that facilitates research in structural bioinformatics and molecular modelling.Written in Python, it consists of: . An object-oriented programming library for manipulating and analyzing macromolecular structures, protein complexes and molecular dynamics trajectories
Rosalind is an educational resource and web project for learning bioinformatics through problem solving and computer programming. [1] [2] [3] Rosalind users learn bioinformatics concepts through a problem tree that builds up biological, algorithmic, and programming knowledge concurrently or learn by topics, with the topic of Alignment, Combinatorics, Computational Mass Spectrometry, Heredity ...
Anyone can either compile an executable from the Python-licensed source code or pay for a subscription to support services to obtain access to precompiled executables. On 8 January 2010, Schrödinger, Inc. reached an agreement to acquire PyMOL. The firm assumed development, maintenance, support, and sales of PyMOL, including all then-valid ...