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PathVisio is a free open-source pathway analysis and drawing software. It allows drawing, editing, and analyzing biological pathways. Visualization of ones experimental data on the pathways for finding relevant pathways that are over-represented in your data set is possible. [1] [2] [3] PathVisio provides a basic set of features for pathway ...
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.
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
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.
Dia has special objects to help draw entity-relationship models, Unified Modeling Language (UML) diagrams, flowcharts, network diagrams, and simple electrical circuits. It is also possible to add support for new shapes by writing simple XML files, using a subset of Scalable Vector Graphics (SVG) to draw the shape.