Tool:Handy online tool for genomic analysis and data visualization - Part II
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Novogene ▴ 130

Previously, I have recommended two powered online tools for genomic analysis and data visualization here. I want to share with you other handy tools that I found recently. iTOL is perfect for beautifying genomic data. circos is useful for displaying the relationships between objects and positions. You could discover their usages below.

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  1. iTOL – Evolutionary Tree Beautification

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In biology and related fields of science, phylogenetic trees are vital tools for contextualization and representation of various data types. iTOL (abbr: interaction Tree Of Life) is an interactive tool that integrates online display, annotation and management of evolutionary trees. iTOL is an online tool that can be accessed with any modern web browser, and it is implemented in pure Javascript. This tool enables users to beautify the phylogenetic tree they aim to construct. As they draw, they can freely adjust the color, shape and font of the branches and labels. iTOL can display different datasets simultaneously and offer customized control of position, size and color according to individual needs. The output can finally be exported as high-quality bitmaps and vector graphics.

iTOL supports different common formats of phylogenetic trees: Newick, Nexus and phyloXML. Phylogenetic placement files and annotation files alike can be uploaded directly and annotated for taxonomic, frequency and sequence alignment visualizations. Any extra data that is relevant can be provided in plain text files, and by simple drag-and-drop mechanism, visualized in the user’s web browser. On top of standard display formats (rectangular, circular and unrooted) the latest version of iTOL supports slanted phylogram display mode as well. The trees such built may be manipulated in several ways, and it is possible to interactively edit by deleting or moving single nodes or whole clades. The clades can be pruned, collapsed and various parameters like branch length distance be adjusted either manually or automatically. Since raw FASTA multiple sequence alignments are also supported by the tool, consensus sequences and residue conservation graphs also can be easily calculated and presented.

Hence, allowing for visualization trees with even more than 50,00 leaves, iTOL is a powerful tool at a biologist’s disposal for beautifying the vast genomic data1. Get access to use at: http://itol.embl.de/index.shtml.

Step 1. Raw File Preparation

Files formats with plain texts only, such as Newick, Nexus, PhyloXML, Text, and Jplace, can be recognized by the tool.

Step 2. Annotation Dataset

Download the annotation templates of evolutionary tree from http://itol.embl.de/help.cgi#annot and prepare datasets accordingly.

Step 3. File Upload

Upload the original phylogenetic tree file to the “Tree file”.

File Upload to the iTOL Figure 1. File Upload to the iTOL

Step 4. Evolutionary diagrams Generation

Users can adjust the parameters based on specific needs, such as display mode, label font, color, line thickness, etc.

Finally, results can be generated like demos!

Bar charts datasets

Figure 2. Bar charts datasets

Protein domain architecture datasets

Figure 3. Protein domain architecture datasets

Color strip datasets

Figure 4. Color strip datasets

Pie chart datasets

Figure 5. Pie chart datasets

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2.circos – circos diagram

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Circos is a command-line software that can be used for visualizing data and information. The online application is suitable for creating rigorously informative infographics with texture and aesthetic appeal. It can create both low-resolution bitmaps for web-page integration, as well as high-resolution publication standard images.

enter image description here

Circos specifically visualize data in a circular layout which makes it the perfect tool for exploring and representing relationships between objects and positions. With its high data-to-ink ratio, circos creates images that are highly attractive. Each element in the image is modular and controllable, and allows the user to tailor the focus points and details catered to the audience’s appeal. Get the figure from http://mkweb.bcgsc.ca/tableviewer/visualize/.

enter image description here

For input, circos takes GFF-style data files and Apache-like configuration files both of which can be easily generated by automated tools. The configuration is modular, and parameter blocks are reusable when imported from multiple files. The output images hence generated can be created in PNG (8 or 24 bit) or SVG formats. Intuitive and easy to play around, circos definitely is a tool that makes a biological scientist’s work more palatable and attractive for a wider audience1. Taking the analysis of the microbial abundance and species diversity as an example, here shows demos to explain the function of drawing the circos diagram.

(1) Data Preparation

The data used are the relative abundance of species in each sample, as follows (S1, S2, S3 are sample names in columns, and Acetobacteraceae, and other species classifications are in rows). Please note that the data formats are required in a non-negative integer.

enter image description here

(2) Diagram Generation & Saving

Upload your data file and click button of “Visualize Table”. Then you will get the Circos image ready. By setting the segments, labels and other parameters, the layout of the images will be optimized based on your own needs.

enter image description here


Sourced from Novogene Website:

https://en.novogene.com/resources/blog/four-powered-online-tools-for-genomic-analysis-and-visualization-evolutionary-tree/

https://en.novogene.com/resources/blog/four-powered-online-tools-for-genomic-analysis-and-visualization-iv-circos/

NGS analysis BI Bioinformatics Sequencing • 135 views
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