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Open Chemistry Project: BEDtools "Genome arithmetic"—manipulation of coordinate sets and the extraction of sequences from a BED file. Linux: MIT: QuinlanLab, University of Utah: Bioclipse: Visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP) Linux, macOS, Windows [1] Eclipse Public: The Bioclipse ...
However, there are relatively few databases dedicated to image collection, although some projects such as iNaturalist collect photos as a main part of their data. A special case of "images" are 3-dimensional images such as protein structures or 3D-reconstructions of anatomical structures. Image databases include, among others: [22] Allen Brain ...
GenMAPP was developed by biologists and is focused on pathway visualization for bench biologists. Unlike many other computational systems biology tools, GenMAPP is not designed for cell/systems modeling; it focuses on the immediate needs of bench biologists by enabling them to rapidly interpret genomic data with an intuitive, easy-to-use interface.
Galaxy [2] is an open-source scientific workflow system designed to make research accessible, reproducible, and transparent. Originally developed for computational biology, Galaxy has evolved into a domain-agnostic framework utilized across various scientific disciplines.
Many free and open-source software tools have existed and continued to grow since the 1980s. [59] The combination of a continued need for new algorithms for the analysis of emerging types of biological readouts, the potential for innovative in silico experiments, and freely available open code bases have created opportunities for research ...
Uses adaptative seeds and copes more efficiently with repeat-rich sequences (e.g. genomes). For example: it can align reads to genomes without repeat-masking, without becoming overwhelmed by repetitive hits. Yes Yes Yes Yes Free, GPL [46] 2011 MAQ Ungapped alignment that takes into account quality scores for each base. Free, GPL: mrFAST, mrsFAST
List of open-source bioinformatics software; Alternatively, here is a categorization according to the respective bioinformatics subfield specialized on: Sequence analysis software. List of sequence alignment software; List of alignment visualization software; Alignment-free sequence analysis; De novo sequence assemblers; List of gene prediction ...
Open-source software. Autodesk Genetic Constructor (suspended) ... Integrative Genomics Viewer (part of Google Genomics) Mengqvist's DNApy; See also