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C++ based molecule editor and visualizer for in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Linux, macOS, Unix, Windows: 3-Clause BSD License: Open Chemistry Project: BEDtools "Genome arithmetic"—manipulation of coordinate sets and the extraction of sequences from a BED file. Linux: MIT
DNASTAR Lasergene Molecular Biology Suite Yes Align DNA, RNA, protein, or DNA + protein sequences via a variety of pairwise and multiple sequence alignment algorithms, generate phylogenetic trees to predict evolutionary relationships, explore sequence tracks to view GC content, gap fraction, sequence logos, translation
Free open source: ms-2.de: OpenMM: No No Yes Yes Yes Yes No Yes Yes High Performance MD, highly flexible, Python scriptable Free open source MIT: OpenMM: Orac: No No Yes Yes No Yes No Yes No Molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomic level Free open source: Orac download page ...
It can be used directly or through mVISTA, Genome VISTA, or VISTA Browser. A database of tissue-specific human enhancers is available through VISTA Enhancer Browser. [1] GenomeVISTA allows the comparison of sequences with whole genome assemblies. It will automatically find the ortholog, obtain the alignment and VISTA plot.
Indexes the genome with a k-mer lookup table with full sensitivity up to an adjustable number of mismatches. It is best for mapping 15-60 bp sequences to a genome. No No Yes No, multiple processes per search 2003 QPalma Can use quality scores, intron lengths, and computation splice site predictions to perform and performs an unbiased alignment.
Animation of molecular activities illustrates the dynamic behaviors of biomolecules, serving as a powerful educational and research tool. Utilizing Unity3D game engine technology, this approach democratizes the creation of interactive molecular visualization tools, resulting in a user-friendly platform that simplifies complex biological data ...
An alignment-free bioinformatics procedure to infer distance-based phylogenetic trees from genome assemblies, specifically designed to quickly infer trees from genomes belonging to the same genus: MinHash-based pairwise genome distance, Balanced Minimum Evolution (BME), ratchet-based BME tree search, Rate of Elementary Quartets: A. Criscuolo ...
Galaxy [2] is a scientific workflow, data integration, [3] [4] and data and analysis persistence and publishing platform that aims to make computational biology and other scientific disciplines accessible to research scientists that do not have computer programming or systems administration experience.