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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.
Proprietary, free use Yes Browser Official website: IVisTMSA No Clustal Omega, ClustalW2, MAFFT, MUSCLE, BioJava are integrated to construct alignment Tree calculation tool calculates phylogenetic tree using BioJava API and lets user draw trees using Archaeopteryx: Software is package of 7 interactive visual tools for multiple sequence alignments.
UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. [1]
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
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.
Link, visualise and explore sequence and meta-data using phylogenetic trees, maps and timelines OneZoom [8] uses IFIG (Interactive Fractal Inspired Graphs) to display phylogenetic trees which can be zoomed in on to increase detail Lifemap [9] Fractal-like representation to provide an interactive explorer of the tree of life "à la google maps"
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 ...
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 ...