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Sliding windows and assembly is a tool chain for folding long series of similar hairpins. No: sourcecode Archived 2012-04-25 at the Wayback Machine [6] SPOT-RNA: SPOT-RNA is first RNA secondary structure predictor which can predict all kind base pairs (canonical, noncanonical, pseudoknots, and base triplets). Yes sourcecode. webserver [35] SwiSpot
Coot is free software, distributed under the GNU GPL. It is available from the Coot web site [ 4 ] originally at the University of York , and now at the MRC Laboratory of Molecular Biology . Pre-compiled binaries are also available for Linux and Windows from the web page and CCP4 , and for Mac OS X through Fink and CCP4.
Software tools for molecular design-Tinker-OpenMM [6] Software tools for molecular design-Tinker-HP [7] Proprietary, gratis Washington University: UCSF Chimera: Yes Yes Yes No No No No No No Visually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development. Proprietary, free ...
Software platform, allows organizations to integrate, analyze, and share complex biomedical data Linux, macOS, Windows: Apache: LabKey Software Foundation LAMMPS: Molecular dynamics program written in C++: Linux, macOS, Windows: Apache: Sandia National Laboratories. mothur: Software for analysis of 16S rRNA gene amplicon sequence data Linux ...
Java-based dot-plot tool: Both: Global: M. Pagni and T. Junier: 1998 FEAST Posterior based local extension with descriptive evolution model: Nucleotide: Local: A. K. Hudek and D. G. Brown: 2010 Genome Compiler Genome Compiler Align chromatogram files (.ab1, .scf) against a template sequence, locate errors, and correct them instantly. Nucleotide ...
Salmon is a software tool for computing transcript abundance from RNA-seq data using either an alignment-free (based directly on the raw reads) or an alignment-based (based on pre-computed alignments) approach. It uses an online stochastic optimization approach to maximize the likelihood of the transcript abundances under the observed data.
MNHN-Tree-Tools is an opensource phylogenetics inference software working on nucleic and protein sequences. Clustering of DNA or protein sequences and phylogenetic tree inference from a set of sequences. At the core it employs a distance-density based approach. Thomas Haschka, Loïc Ponger, Christophe Escudé and Julien Mozziconacci [28 ...
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