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Linux, macOS, Windows: BSD: Laura Luebbert and Lior Pachter: GROMACS: Molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. Linux, macOS, Windows: Common Public 1.0 GenoViz Integrated Genome Browser: Java-based desktop genome browser: Linux, macOS, Windows: Common Public 1.0 GenoViz InterMine
NEMO 3-D [10] – enables multi-million atom electronic structure simulations in empirical tight binding; open source; an educational version is on nanoHUB and Quantum Dot Lab [11] nextnano [12] allows simulating geometry, electronic properties and electrical transport phenomena in various nanostructures using continuum models (commercial software)
Agilent Technologies RFLP Decoder Software, Fish Species; Applied Biosystems GeneMapper; Joint BioEnergy Institute j5; CLC bio CLC DNA Workbench Software; CLC bio CLC Free Workbench Software; CLC bio CLC Sequence Viewer; CLC bio Protein Workbench Software; DNASTAR Lasergene; Geneious; LabVantage Solutions Inc. LabVantage Sapphire; LabVantage ...
Molecular design software; Molecule editor; Quantum chemistry computer programs; List of molecular graphics systems; List of protein structure prediction software; List of sequence alignment software; List of gene prediction software; List of RNA structure prediction software; Comparison of software for molecular mechanics modeling
[10] 2001 / 2018 OS link: DISCOVAR paired-end PCR-free reads (successor of ALLPATHS-LG) Illumina (MiSeq or HiSeq 2500) [11] 2014 OS link: DNA Baser Sequence Assembler DNA sequence assembly with automatic end trimming & ambiguity correction. Includes a base caller. Sanger, Illumina Heracle BioSoft SRL 2018.09 C ($69) NA DNASTAR Lasergene Genomics
Molecular models are useful in the design of structures for DNA nanotechnology. Here, individual DNA tiles (model at left) self-assemble into a highly ordered DNA 2D-nanogrid (AFM image at right). There are various uses of DNA molecular modeling in Genomics and Biotechnology research applications, from DNA repair to PCR and DNA nanostructures.
DNA nanotechnology, specifically, is an example of bottom-up molecular self-assembly, in which molecular components spontaneously organize into stable structures; the particular form of these structures is induced by the physical and chemical properties of the components selected by the designers. [19]
DNADynamo is a general purpose DNA and Protein sequence analysis package that can carry out most of the functions required by a standard research molecular biology laboratory DNA and Protein Sequence viewing, editing and annotating; Contig assembly and chromatogram editing including comparison to a reference sequence to identify mutations