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PlasMapper (Plasmid Mapper) [1] is a freely available web server that automatically generates and annotates high-quality circular plasmid maps. It is a particularly useful online service for molecular biologists wishing to generate plasmid maps without having to purchase or maintain expensive, commercial software.
It can map Illumina and SOLiD reads. Unlike most mapping programs, speed increases for longer read lengths. Yes Free, GPL [49] PRIMEX 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
UGENE is computer software for bioinformatics. [1] [2] It works on personal computer operating systems such as Windows, macOS, or Linux.It is released as free and open-source software, under a GNU General Public License (GPL) version 2.
Free, GPL 2 Yes Browser Official website: Lucid Align No No No Native desktop alignment viewer, uses trackpad/mouse gestures. Allows streaming remote data BAM, FASTQ, FASTA Proprietary, commercial, freeware for academic use No Mac OS Official website: Maestro Yes ClustalX Yes Mapping from sequence to 3D structure, structure-sequence editing ...
Molecular biology tools. Vector Database—A curated list of over 4,000 vector backbones, including relevant cloning information and bacterial growth conditions.. Sequence Analyzer—An Addgene software tool for creating plasmid maps from sequences with annotated features and restriction sites.
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 ...
Proprietary, free academic use, source code Beckman Institute: NWChem: No No Yes Yes No No Yes No No High-performance computational chemistry software, includes quantum mechanics, molecular dynamics and combined QM-MM methods Free open source, Educational Community License version 2.0 NWChem: Protein Local Optimization Program: No Yes Yes Yes ...
MicrobeTrace is a free, browser-based web application. 2D and 3D network visualization tool, Neighbor-joining tree visualization, Gantt charts, bubbles charts, networks visualized on maps, flow diagrams, aggregate tables, epi curves, histograms, alignment viewer, and much more.