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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.
Its principal advantages are (1) easy extension and combination with other libraries due to modular library design, (2) a single high-level general-purpose programming language (Python) is used for library implementation as well as for application scripts, (3) use of documented and machine-independent formats for all data files, and (4 ...
Open Bioinformatics Foundation: Biopython: Python language toolkit Cross-platform: Biopython [2] Open Bioinformatics Foundation: BioRuby: Ruby language toolkit Linux, macOS, Windows [3] GPL v2 or Ruby: Open Bioinformatics Foundation: BLAST: Algorithm and program for comparing primary biological sequence information, including DNA and protein ...
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]
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 ...
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
Python tool for modeling and analyzing SBML models [21] [22] [23] multiplatform (Python) BSD-3: Yes pySB: Python-based [24] platform with specialization in rule-based models. multiplatform (Python) BSD-3: Partial ReaDDy: Particle-based spatial simulator with intermolecular potentials [25] Linux and Mac: Custom: Not applicable SBSCL
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.