Results for "Visualization"
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Bandage: interactive visualization of de novo genome assemblies
Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes, adding labels, changing colors and extracting sequ...Tags: Bandage, interactive, visualization, de novo, genome, assemblies
2341 days ago
Harvest: a suite of core-genome alignment and visualization tools
Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees. Tools Parsnp - Core-genome alignment and analysis Gingr - Interactive ...Tags: Harvest, alignment, visualization, intraspecific, microbial, genomes, recombination, detection, phylogenetic, trees
2337 days ago
Delta: a new Web-based 3D genome visualization and analysis platform
Delta is an integrative visualization and analysis platform to facilitate visually annotating and exploring the 3D physical architecture of genomes. Delta takes Hi-C or ChIA-PET contact matrix as input and predicts the topologically associating domains and chromatin loops in the ge...Tags: Delta, Web-based, 3D, genome, visualization, analysis, platform
2325 days ago
zPicture: A dynamic blastz alignment visualization
zPicture is a dynamic alignment and visualization tool that is based on blastz alignment program utilized by PipMaker. zPicture alignments can be automatically submitted to rVista 2.0 to identify conserved transcription factor binding sites.Tags: zPicture, dynamic, blastz, alignment, visualization
2284 days ago
xmatchview: smith-waterman alignment visualization
xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between DNA sequences. It allows users to align 2 DNA sequences in fasta format using cross_match and displays the alignment in a variety of image formats. xmatchview and xmatchview-conifer are written in python and run...Tags: xmatchview, smith-waterman, alignment, visualization, synteny
2317 days ago
AliTV—interactive visualization of whole genome comparisons
AliTV, which provides interactive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are supported. The user-friendly, web-browser based an...Tags: AliTV, interactive, visualization, whole, genome, comparisons
2304 days ago
G-compass: a comparative genome browser
G-compass (http://www.h-invitational.jp/g-compass/) is a comparative genome browser. It visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage (1,2). Annotations of human genes/transcripts and their o...Tags: G-compass, comparative, genome, browser, visualization
2212 days ago
- Download and install MUMmer Align your assembly to a reference genome using nucmer (from MUMmer package) $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT Consult the MUMmer manual if you encounter problems Optional: Gzip the delta file to speed up upload (usually 2-4X f...
Tags: assemblytics, delta, analyze, alignment, assembly, reference, genome, visualization
2149 days ago
Epiviz: an interactive visualization tool for functional genomics data.
Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. It also includes data from the...Tags: Epiviz, interactive, visualization, tool, functional, genomics, data
2124 days ago
Genome U-Plot: a whole genome visualization
Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution an...Tags: Genome, U-Plot, whole, genome, visualization
2119 days ago
