{"id":23843,"date":"2021-08-12T23:50:16","date_gmt":"2021-08-13T06:50:16","guid":{"rendered":"https:\/\/www.novogene.com\/us-en\/?post_type=resources&#038;p=23843"},"modified":"2025-05-29T03:39:47","modified_gmt":"2025-05-29T10:39:47","slug":"four-powered-online-tools-for-genomic-analysis-and-visualization-evolutionary-tree","status":"publish","type":"resources","link":"https:\/\/www.novogene.com\/us-en\/resources\/blog\/four-powered-online-tools-for-genomic-analysis-and-visualization-evolutionary-tree\/","title":{"rendered":"Four Powered Online Tools for Genomic Analysis and Visualization (III) \u2013 iTOL"},"content":{"rendered":"<h5>III. iTOL &#8211; Evolutionary Tree Beautification<\/h5>\n<p>In biology and related fields of science, phylogenetic trees are vital tools for contextualization and representation of various data types. <strong>iTOL<\/strong> (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. <\/p>\n<p>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\u2019s 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.<\/p>\n<p>Hence, allowing for visualization trees with even more than 50,00 leaves, iTOL is a powerful tool at a biologist\u2019s disposal for beautifying the vast genomic data[1]. Get access to use at: <a href=\"http:\/\/itol.embl.de\/index.shtml\" target=\"_blank\" rel=\"noopener noreferrer\">http:\/\/itol.embl.de\/index.shtml<\/a>.<\/p>\n<p><strong>Step 1. Raw File Preparation<\/strong><br \/>\nFiles formats with plain texts only, such as Newick, Nexus, PhyloXML, Text, and Jplace, can be recognized by the tool.<\/p>\n<p><strong>Step 2. Annotation Dataset<\/strong><br \/>\nDownload the annotation templates of evolutionary tree from <a href=\"http:\/\/itol.embl.de\/help.cgi#annot\" target=\"_blank\" rel=\"noopener noreferrer\">http:\/\/itol.embl.de\/help.cgi#annot<\/a> and prepare datasets accordingly.<\/p>\n<p><strong>Step 3. File Upload<\/strong><br \/>\nUpload the original phylogenetic tree file to the \u201cTree file\u201d.<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.novogene.com\/us-en\/wp-content\/uploads\/sites\/4\/2021\/08\/20210813143226.png\" alt=\"\" class=\"img_jz\" \/><\/p>\n<p style=\"text-align:center;font-weight:bold;\">Figure 1. File Upload to the iTOL<\/p>\n<p><strong>Step 4. Evolutionary diagrams Generation<\/strong><br \/>\nUsers can adjust the parameters based on specific needs, such as display mode, label font, color, line thickness, etc. <\/p>\n<p>Finally, results can be generated like demos!<\/p>\n<div style=\"width:50%;float:left;\">\n\t<img decoding=\"async\" src=\"https:\/\/www.novogene.com\/us-en\/wp-content\/uploads\/sites\/4\/2021\/08\/20210813143246.png\" alt=\"\" class=\"img_jz\" \/><\/p>\n<p style=\"text-align:center;font-weight:bold;\">Figure 2. Bar charts datasets<\/p>\n<\/div>\n<div style=\"width:50%;float:right;\">\n\t<img decoding=\"async\" src=\"https:\/\/www.novogene.com\/us-en\/wp-content\/uploads\/sites\/4\/2021\/08\/20210813143235.png\" alt=\"\" class=\"img_jz\" \/><\/p>\n<p style=\"text-align:center;font-weight:bold;\">Figure 3. Protein domain architecture datasets<\/p>\n<\/div>\n<div style=\"clear:both;height:20px;\"><\/div>\n<div style=\"width:50%;float:left;\">\n\t<img decoding=\"async\" src=\"https:\/\/www.novogene.com\/us-en\/wp-content\/uploads\/sites\/4\/2021\/08\/20210813143240.png\" alt=\"\" class=\"img_jz\" \/><\/p>\n<p style=\"text-align:center;font-weight:bold;\">Figure 4. Color strip datasets<\/p>\n<\/div>\n<div style=\"width:50%;float:right;\">\n\t<img decoding=\"async\" src=\"https:\/\/www.novogene.com\/us-en\/wp-content\/uploads\/sites\/4\/2021\/08\/20210813143252.png\" alt=\"\" class=\"img_jz\" \/><\/p>\n<p style=\"text-align:center;font-weight:bold;\">Figure 5. Pie chart datasets.<\/p>\n<\/div>\n<div style=\"clear:both;height:20px;\"><\/div>\n<p><strong>Reference <\/strong><br \/>\n[1] Letunic, I., &#038; Bork, P. (2019). Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic acids research, 47(W1), W256\u2013W259. <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkz239\" target=\"_blank\" rel=\"noopener noreferrer\">https:\/\/doi.org\/10.1093\/nar\/gkz239<\/a><\/p>\n","protected":false},"featured_media":0,"parent":0,"template":"","yoast_head":"<!-- This site is optimized with the Yoast SEO Premium plugin v20.8 (Yoast SEO v20.8) - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Four Powered Online Tools for Genomic Analysis and Visualization (III) \u2013 iTOL - Novogene<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.novogene.com\/us-en\/resources\/blog\/four-powered-online-tools-for-genomic-analysis-and-visualization-evolutionary-tree\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Four Powered Online Tools for Genomic Analysis and Visualization (III) \u2013 iTOL\" \/>\n<meta property=\"og:description\" content=\"III. iTOL &#8211; Evolutionary Tree Beautification 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\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.novogene.com\/us-en\/resources\/blog\/four-powered-online-tools-for-genomic-analysis-and-visualization-evolutionary-tree\/\" \/>\n<meta property=\"og:site_name\" content=\"Novogene\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/NovogeneAmerica\/\" \/>\n<meta property=\"article:modified_time\" content=\"2025-05-29T10:39:47+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.novogene.com\/us-en\/wp-content\/uploads\/sites\/4\/2021\/08\/20210813143226.png\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:site\" content=\"@Novogene_Global\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"3 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/www.novogene.com\/us-en\/resources\/blog\/four-powered-online-tools-for-genomic-analysis-and-visualization-evolutionary-tree\/\",\"url\":\"https:\/\/www.novogene.com\/us-en\/resources\/blog\/four-powered-online-tools-for-genomic-analysis-and-visualization-evolutionary-tree\/\",\"name\":\"Four Powered Online Tools for Genomic Analysis and Visualization (III) \u2013 iTOL - Novogene\",\"isPartOf\":{\"@id\":\"https:\/\/www.novogene.com\/us-en\/#website\"},\"datePublished\":\"2021-08-13T06:50:16+00:00\",\"dateModified\":\"2025-05-29T10:39:47+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/www.novogene.com\/us-en\/resources\/blog\/four-powered-online-tools-for-genomic-analysis-and-visualization-evolutionary-tree\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/www.novogene.com\/us-en\/resources\/blog\/four-powered-online-tools-for-genomic-analysis-and-visualization-evolutionary-tree\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/www.novogene.com\/us-en\/resources\/blog\/four-powered-online-tools-for-genomic-analysis-and-visualization-evolutionary-tree\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/www.novogene.com\/us-en\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Resources\",\"item\":\"https:\/\/www.novogene.com\/us-en\/resources\/\"},{\"@type\":\"ListItem\",\"position\":3,\"name\":\"Four Powered Online Tools for Genomic Analysis and Visualization (III) \u2013 iTOL\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/www.novogene.com\/us-en\/#website\",\"url\":\"https:\/\/www.novogene.com\/us-en\/\",\"name\":\"Novogene\",\"description\":\"USA Based Lab Guaranteed Data Security\",\"publisher\":{\"@id\":\"https:\/\/www.novogene.com\/us-en\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/www.novogene.com\/us-en\/?s={search_term_string}\"},\"query-input\":\"required name=search_term_string\"}],\"inLanguage\":\"en-US\"},{\"@type\":\"Organization\",\"@id\":\"https:\/\/www.novogene.com\/us-en\/#organization\",\"name\":\"Novogene\",\"url\":\"https:\/\/www.novogene.com\/us-en\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/www.novogene.com\/us-en\/#\/schema\/logo\/image\/\",\"url\":\"https:\/\/www.novogene.com\/us-en\/wp-content\/uploads\/sites\/4\/2020\/05\/20200506113246.png\",\"contentUrl\":\"https:\/\/www.novogene.com\/us-en\/wp-content\/uploads\/sites\/4\/2020\/05\/20200506113246.png\",\"width\":941,\"height\":269,\"caption\":\"Novogene\"},\"image\":{\"@id\":\"https:\/\/www.novogene.com\/us-en\/#\/schema\/logo\/image\/\"},\"sameAs\":[\"https:\/\/www.facebook.com\/NovogeneAmerica\/\",\"https:\/\/twitter.com\/Novogene_Global\",\"https:\/\/www.linkedin.com\/company\/novogene\/\",\"https:\/\/www.youtube.com\/c\/NovogeneGlobal\"]}]}<\/script>\n<!-- \/ Yoast SEO Premium plugin. -->","yoast_head_json":{"title":"Four Powered Online Tools for Genomic Analysis and Visualization (III) \u2013 iTOL - Novogene","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.novogene.com\/us-en\/resources\/blog\/four-powered-online-tools-for-genomic-analysis-and-visualization-evolutionary-tree\/","og_locale":"en_US","og_type":"article","og_title":"Four Powered Online Tools for Genomic Analysis and Visualization (III) \u2013 iTOL","og_description":"III. iTOL &#8211; 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