A web app and library for visualising and comparing phylogenetic trees.
The app can be accessed at beta.phylo.io.
For any bugs, features requests or help for integration please contact us through github.
CDN: The easiest way to get started is to use the CDN. You need to first import the two worker files then the main phylo.js file. You also need to import the CSS file for the UI icon.
<!-- Boostrap Icon -->
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.5.0/font/bootstrap-icons.css">
<!-- Phylo.io Bundle -->
<script src="https://cdn.jsdelivr.net/gh/DessimozLab/phylo-io@master/dist/src_worker_bcn_js.phylo.js"></script>
<script src="https://cdn.jsdelivr.net/gh/DessimozLab/phylo-io@master/dist/src_worker_distance_js.phylo.js"></script>
<script src="https://cdn.jsdelivr.net/gh/DessimozLab/phylo-io@master/dist/phylo.js"></script>Easy: Import all the pre generated js files from the dist/ folder frm this repository. The main library is bundle into phylo.js. The two other files src_worker_*.js contains the web workers for the distance and bcn algorithms.
<!-- Boostrap Icon -->
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.5.0/font/bootstrap-icons.css">
<script src="path/to/dist/src_worker_bcn_js.js"></script>
<script src="path/to/dist/src_worker_distance_js.js"></script>
<script src="path/to/dist/phylo.js"></script>Local build: If you need to modify part of the source code or simply want to build the package from source, you can use the following command
npm run-script buildThis will build the dist/ folder where you can import the *.js files as shown above.
First, you need to create an instance of PhyloIO:
const phylo = PhyloIO.init() Then, you need to instantiate a container (or viewer) inside a div:
const c1 = phylo.create_container("div_id")If you want to compare several trees, you need to provide two containers:
const c1 = phylo.create_container("div_id_1")
const c2 = phylo.create_container("div_id_2")
// Required parameters for compare mode
phylo.settings.compareMode = true;
phylo.bound_container = [c1,c2];Optional: you can already add trees into containers
const newick1 = "((yli:1.0085614391793067,(((lel:0.2880678599618948,(cal:0.11643570498932501,ctr:0.12746420698315983):0.0877413194006926):0.12449843844102518,pst:0.20187483296288805):0.04951181210826987,(pgu:0.3208350693977453,dha:0.19121342958249643):0.0444880656387921):0.3761988962574594):0.22545281705785974,(((kla:0.32829009627835226,ago:0.35217085340006204):0.057415467336693615,(skl:0.15813405639248146,kwa:0.25658337062111586):0.04348414441988464):0.036897766465122404,(cgl:0.29957965624763355,(sca:0.24212307199678842,(sba:0.03984952076326609,(((sce:0.022286259220280224,spa:0.016875934069075366):0.01282179619059339,smi:0.03661027033511007):0.013312280806766753,sku:0.042685124078088485):0.014142671709463695):0.17548658899657893):0.03625000527459598):0.08921537612721808):0.22545281705785974):0;"
const newick2 = 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var SETTINGS = {'use_branch_lenght': true, 'name': 'tree #1'}
c1.add_tree(newick1, SETTINGS )
c2.add_tree(newick2)Here are settings you can specify when adding a tree ('SETTINGS' in the example above):
'display_leaves' : true,
'display_nodes_labels' : true,
'mirror': false,
'name': null,
'data_type' : 'newick',
'use_branch_lenght' : true,
'show_tooltips' : false,
'subsample_label' : true,
'display_internal_label' : false,
'display_internal_label_left_top' : false,
'display_internal_label_left_bottom' : false,
'display_leaf_label' : false,
'display_leaf_label_left_top' : false,
'display_leaf_label_left_bottom' : false,
'display_duplication' : false,
'show_histogram' : false,
'align_tip' : false,
'tree': {
'node_vertical_size' : 30,
'node_horizontal_size' : 40,
'node_radius' : 6,
'line_width' : 3,
'font_size':14,
},
'collapse_level': 0Finally, you can start phylo.io:
phylo.start()As shown in 'Examples/Phylo Stack', you can display phylostratigraphy viewer by doing:
var custom_settings = {
'name': 'phylostratigraphy',
'data_type' : 'json',
'use_branch_lenght' : false,
'show_histogram' : true,
'has_histogram_data' : true,
'stack' : {
'type': 'genes',// or 'events',
'showHistogramValues' : false,
'showHistogramSummaryValue' : true,
'legendTxtSize' : 12,
'margin' : 8,
'xInitialRightMargin' : 25,
'stackHeight' : 50,
'stackWidth' : 50,
'maxStackHeight': 'max', // ratio -> stack height fixed | max -> largest data = stack height
},
}
const tree_stack = {"children": [{"children": [{"children": [{"children": [{"id": "HALHT", "last_updated": "Aug 20, 2012", "name": "Haloarcula hispanica (strain ATCC 33960 / DSM 4426 / JCM 8911 / NBRC 102182 / NCIMB 2187 / VKM B-1755)", "nr_proteins": 3855, "release": "18-OCT-2011 (Rel. 110, Last updated, Version 2)", "source": "EBI", "taxid": 634497}, {"id": "HALMA", "last_updated": "Mar 25, 2014", "name": "Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)", "nr_proteins": 4231, "release": "02-FEB-2014 (Rel. 119, Last updated, Version 9)", "source": "EBI", "taxid": 272569}], "name": "Haloarcula", "taxid": 2237, "nr_hogs": 4107, "evolutionaryEvents": {"gained": 178, "retained": 3532, "duplicated": 397, "lost": 1508, "duplications": 166}}, {"id": "HALMD", "last_updated": "Nov 23, 2009", "name": "Halomicrobium mukohataei (strain ATCC 700874 / DSM 12286 / JCM 9738 / NCIMB 13541)", "nr_proteins": 3168, "release": "03-NOV-2009 (Rel. 113, Last updated, Version 1)", "source": "Genome Reviews", "taxid": 485914}, {"id": "HALUD", "last_updated": "Nov 23, 2009", "name": "Halorhabdus utahensis (strain DSM 12940 / JCM 11049 / AX-2)", "nr_proteins": 2998, "release": "03-NOV-2009 (Rel. 113, Last updated, Version 1)", "source": "Genome Reviews", "taxid": 519442}, {"children": [{"id": "NATM8", "last_updated": "Oct 27, 2014", "name": "Natronomonas moolapensis (strain DSM 18674 / JCM 14361 / 8.8.11)", "nr_proteins": 2852, "release": "27-FEB-2014 (Rel. 119, Last updated, Version 4)", "source": "EBI", "taxid": 268739}, {"id": "NATPD", "last_updated": "Mar 25, 2014", "name": "Natronomonas pharaonis (strain ATCC 35678 / DSM 2160 / CIP 103997 / NBRC 14720 / NCIMB 2260 / Gabara)", "nr_proteins": 2824, "release": "07-MAR-2014 (Rel. 120, Last updated, Version 14)", "source": "EBI", "taxid": 348780}], "name": "Natronomonas", "taxid": 63743, "nr_hogs": 3156, "evolutionaryEvents": {"gained": 93, "lost": 2294, "duplicated": 254, "retained": 2809, "duplications": 103}}], "name": "Haloarculaceae", "taxid": 1963268, "nr_hogs": 5206, "evolutionaryEvents": {"gained": 273, "retained": 4584, "duplicated": 349, "lost": 1040, "duplications": 163}}, {"children": [{"id": "HALJB", "last_updated": "Dec 23, 2010", "name": "Halalkalicoccus jeotgali (strain DSM 18796 / CECT 7217 / JCM 14584 / KCTC 4019 / B3)", "nr_proteins": 3779, "release": "30-NOV-2010 (Rel. 127, Last updated, Version 2)", "source": "Genome Reviews", "taxid": 795797}, {"children": [{"id": "HALS3", "last_updated": "May 8, 2008", "name": "Halobacterium salinarum (strain ATCC 29341 / DSM 671 / R1)", "nr_proteins": 2742, "release": "29-APR-2008 (Rel. 90, Last updated, Version 1)", "source": "Genome Reviews", "taxid": 478009}, {"id": "HALSA", "last_updated": "Mar 25, 2014", "name": "Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)", "nr_proteins": 2418, "release": "03-FEB-2014 (Rel. 119, Last updated, Version 7)", "source": "EBI", "taxid": 64091}], "name": "Halobacterium salinarum", "taxid": 2242, "nr_hogs": 2540, "evolutionaryEvents": {"gained": 201, "retained": 2202, "duplicated": 137, "lost": 1437, "duplications": 62}}], "name": "Halobacteriaceae", "taxid": 2236, "nr_hogs": 3701, "evolutionaryEvents": {"gained": 13, "retained": 3605, "duplicated": 83, "lost": 2142, "duplications": 40}}], "name": "Halobacteriales", "taxid": 2235, "nr_hogs": 5787, "evolutionaryEvents": {"gained": 118, "retained": 5120, "lost": 1677, "duplicated": 549, "duplications": 228}}, {"children": [{"children": [{"children": [{"id": "HALMT", "last_updated": "Nov 30, 2012", "name": "Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4)", "nr_proteins": 3861, "release": "02-AUG-2012 (Rel. 113, Last updated, Version 3)", "source": "EBI", "taxid": 523841}, {"id": "HALVD", "last_updated": "Jul 20, 2010", "name": "Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2)", "nr_proteins": 3986, "release": "13-JUL-2010 (Rel. 123, Last updated, Version 2)", "source": "Genome Reviews", "taxid": 309800}], "name": "Haloferax", "taxid": 2251, "nr_hogs": 4166, "evolutionaryEvents": {"gained": 107, "retained": 3786, "lost": 1192, "duplicated": 273, "duplications": 108}}, {"id": "HALBP", "last_updated": "Aug 20, 2012", "name": "Halogeometricum borinquense (strain ATCC 700274 / DSM 11551 / JCM 10706 / PR3)", "nr_proteins": 3894, "release": "24-NOV-2010 (Rel. 106, Last updated, Version 1)", "source": "EBI", "taxid": 469382}, {"children": [{"id": "HALWD", "last_updated": "Sep 26, 2006", "name": "Haloquadratum walsbyi (strain DSM 16790 / HBSQ001)", "nr_proteins": 2819, "release": "24-JUL-2006 (Rel. 88, Last updated, Version 2)", "source": "EBI", "taxid": 362976}, {"id": "HALWC", "last_updated": "Apr 2, 2012", "name": "Haloquadratum walsbyi (strain DSM 16854 / JCM 12705 / C23)", "nr_proteins": 2974, "release": "15-MAR-2012 (Rel. 112, Last updated, Version 4)", "source": "EBI", "taxid": 768065}], "name": "Haloquadratum walsbyi", "taxid": 293091, "nr_hogs": 2819, "evolutionaryEvents": {"gained": 209, "retained": 2443, "lost": 2564, "duplicated": 167, "duplications": 79}}], "name": "Haloferacaceae", "taxid": 1644056, "nr_hogs": 5086, "evolutionaryEvents": {"gained": 222, "duplicated": 385, "retained": 4479, "lost": 571, "duplications": 174}}, {"id": "HALLT", "last_updated": "Jun 22, 2009", "name": "Halorubrum lacusprofundi (strain ATCC 49239 / DSM 5036 / JCM 8891 / ACAM 34)", "nr_proteins": 3493, "release": "16-JUN-2009 (Rel. 107, Last updated, Version 3)", "source": "Genome Reviews", "taxid": 416348}], "name": "Haloferacales", "taxid": 1644055, "nr_hogs": 5224, "evolutionaryEvents": {"gained": 94, "retained": 4671, "lost": 2155, "duplicated": 459, "duplications": 199}}, {"children": [{"id": "HALXS", "last_updated": "Aug 20, 2012", "name": "Halopiger xanaduensis (strain DSM 18323 / JCM 14033 / SH-6)", "nr_proteins": 4221, "release": "23-NOV-2011 (Rel. 110, Last updated, Version 2)", "source": "EBI", "taxid": 797210}, {"id": "HALTV", "last_updated": "Jun 11, 2010", "name": "Haloterrigena turkmenica (strain ATCC 51198 / DSM 5511 / NCIMB 13204 / VKM B-1734)", "nr_proteins": 3739, "release": "25-MAY-2010 (Rel. 121, Last updated, Version 2)", "source": "Genome Reviews", "taxid": 543526}, {"id": "HALRX", "last_updated": "Dec 18, 2013", "name": "Halovivax ruber (strain DSM 18193 / JCM 13892 / XH-70)", "nr_proteins": 3099, "release": "18-JUL-2013 (Rel. 117, Last updated, Version 2)", "source": "EBI", "taxid": 797302}, {"children": [{"id": "NATA1", "last_updated": "Aug 10, 2017", "name": "Natrialba asiatica (strain ATCC 700177 / DSM 12278 / JCM 9576 / FERM P-10747 / NBRC 102637 / 172P1)", "nr_proteins": 4176, "release": "Ensembl Bacteria 36; ASM33755v1", "source": "EnsemblGenomes", "taxid": 29540}, {"id": "NATMM", "last_updated": "Jul 20, 2010", "name": "Natrialba magadii (strain ATCC 43099 / DSM 3394 / CIP 104546 / JCM 8861/ NBRC 102185 / NCIMB 2190 / MS3)", "nr_proteins": 3558, "release": "13-JUL-2010 (Rel. 123, Last updated, Version 2)", "source": "Genome Reviews", "taxid": 547559}], "name": "Natrialba", "taxid": 63742, "nr_hogs": 4283, "evolutionaryEvents": {"gained": 51, "lost": 2216, "retained": 3820, "duplicated": 412, "duplications": 148}}, {"children": [{"id": "NATP1", "last_updated": "Oct 27, 2014", "name": "Natrinema pellirubrum (strain DSM 15624 / CIP 106293 / JCM 10476 / NCIMB 786 / 157)", "nr_proteins": 4138, "release": "23-JUL-2013 (Rel. 117, Last updated, Version 2)", "source": "EBI", "taxid": 797303}, {"id": "NATSJ", "last_updated": "Oct 27, 2014", "name": "Natrinema sp. (strain J7-2)", "nr_proteins": 4296, "release": "15-MAY-2014 (Rel. 120, Last updated, Version 6)", "source": "EBI", "taxid": 406552}], "name": "Natrinema", "taxid": 88723, "nr_hogs": 4304, "evolutionaryEvents": {"gained": 52, "retained": 3748, "lost": 2241, "duplicated": 504, "duplications": 195}}, {"id": "NATGS", "last_updated": "Oct 27, 2014", "name": "Natronobacterium gregoryi (strain ATCC 43098 / DSM 3393 / CCM 3738 / CIP 104747 / JCM 8860 / NBRC 102187 / NCIMB 2189 / SP2)", "nr_proteins": 3624, "release": "18-JUL-2013 (Rel. 117, Last updated, Version 2)", "source": "EBI", "taxid": 797304}], "name": "Natrialbaceae", "taxid": 1644061, "nr_hogs": 6184, "evolutionaryEvents": {"gained": 842, "duplicated": 729, "retained": 4613, "lost": 2106, "duplications": 306}}], "name": "Halobacteria", "taxid": 183963, "nr_hogs": 7025, "evolutionaryEvents": {"gained": 2357, "lost": 6118, "retained": 2767, "duplicated": 1901, "duplications": 605}}
c1.add_tree(tree_stack,custom_settings)
phylo.start()Welcome to the Phylo.io Help Section. This guide will explain the features of Phylo.io and how to use them effectively.
Phylo.io is a state-of-the-art tool designed for visualizing and comparing phylogenetic trees. It provides an easy-to-use interface for exploring and analyzing phylogenetic data:
- Interactive Tree Viewer: Phylo.io allows you to visualize phylogenetic trees in an interactive format. You can zoom, pan, and click on nodes to explore the tree structure.
- Tree Comparison: You can compare two phylogenetic trees side by side, making it easier to identify differences and similarities between them.
- File Support: Phylo.io supports various file formats, including newick, extended newick and phyloxml making it versatile for different data sources.
- Export Options: You can annotate and configure trees with additional information and export your work in various formats, such as SVG or PNG.
- Mapping Files: Phylo.io allows you to upload mapping files that contain additional data, which can be displayed on the phylogenetic tree. This feature is useful for coloring leaves and branches based on specific attributes.
- Tree Customization: Phylo.io provides options to adjust tree dimensions, branch and label sizes, and colors. You can also choose to display data at internal nodes and customize the appearance of the tree.
- Viewing Large Trees: Phylo.io offers features like label subsampling, autocollapse, and "Fit Tree into Viewer" to help manage large trees effectively. These features enhance the usability of the tool when dealing with complex phylogenetic data.
- Phylo Stack: Phylo.io includes a phylostratigraphy viewer that allows you to visualize and analyze the evolutionary history of genes or events. This feature is particularly useful for researchers studying gene evolution and phylogenetic relationships.
- Settings: Phylo.io allows you to customize various settings, including tree height, width, node radius, line width, leaf label size, and branch coloring. This flexibility enables you to tailor the visualization to your preferences and analysis requirements.
Upload your phylogenetic tree by clicking on “+ Add tree” in the upper right-hand corner of the landing page.
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Step 1: Add data from text or file. Here, you can paste a text string of your tree or upload a tree from a file. Newick, extended newick and phyloxml files are accepted.
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Step 2: Select the tree format.
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Step 3 (Optional): Add a Mapping file. Mapping files contain additional data which can be displayed on the phylogenetic tree. This can be used for coloring leaves and/or branches of the tree. Mapping file requirements:
- Must be in csv or tsv format
- Must contain column headers as the first row
- Must contain a column with name which matches the leaf/internal node names. By default, the column is named ‘id’ but can be change using the dropdown.
- Mapping files can contain categorical or numerical data. Categorical data allows coloring by qualitative color palettes; numerical data allows for coloring by quantitative color spectra. The column data types should be configured in the Mapping file configuration step.
- Additionally, there may be a column that contains colors; these can be the standard color names (supported by matplotlib), Hex, or RGB color codes. The color column must be specified in the Mapping file configuration step.
Once the tree is loaded and displayed, the tree can be navigated by panning, or zooming in/out with the mouse or by the buttons on the lower right side. Searching the tree is possible using the search box in the upper right corner.
Tree Topology can be adjusted using following controls (clicking on the nodes or branches):
- Reroot a tree by clicking on a branch you want to be the outgroup and clicking “Reroot”
- Remove a subtree by clicking on the branch leading to that subtree and clicking “Trim subtree”
- Swap subtrees by clicking on an internal node and clicking “Swap subtrees”
- Collapse subtrees by clicking on an internal node and clicking “Collapse”
- Expand a collapsed subtree by clicking on the internal node or triangle and clicking “Expand” (...) or “Expand all” (...)
Tree dimensions/layout can be adjusted using following controls (Settings -> Tree):
- Switch between cladogram view and view with branch lengths as defined in the newick by the Use branch lengths toggle.
- Align leaves to one side with the Align leaves toggle
- Flip the tree horizontally with the Mirror tree toggle.
- Adjust the Tree height (i.e. control the spacing between leaves) with the -50%, -20%, +20%, and +50% buttons.
- Adjust the Tree width (i.e. scale the branch lengths) with the -50%, -20%, +20%, and +50% buttons.
- Choose the depth at which to autocollapse subtrees with the Autocollapse slider. The depth is the number of edges from the root to a given node.
- For more tips on viewing large trees, see the next section, “Viewing Large Trees”
Branches and labels can be adjusted using following controls (Settings -> Branches & Labels):
- Choose what to display at internal nodes by using the drop-down menu to select the data. The data can be displayed to the upper left, bottom left, or center right of the node.
- To display all the labels and not subsample them automatically with the Subsample Labels toggle.
- Turn on or off the leaf labels with the Show Leaf Labels toggle.
- Display the data associated with each branch/leaf with the Show tooltips toggle.
- Adjust the Node radius (i.e. size with the internal nodes) with the -50%, -20%, +20%, and +50% buttons.
- Adjust the Line width (i.e. size with the thickness of the branches) with the -50%, -20%, +20%, and +50% buttons.
- Adjust the Leaf label size (i.e. font size of the leaves) with the -50%, -20%, +20%, and +50% buttons.
- Adjust the Node label size (i.e. font size of the internal node labels) with the -50%, -20%, +20%, and +50% buttons.
Coloring the tree can be customized using following controls (Settings -> Coloring): Adjust the color of the leaves and/or branches using data from the extended newick or in the Mapping file. After choosing data to display, if the data is categorical, you can choose the color loaded as a column or one of the preloaded color palettes. If the data is numerical, you can choose your color spectrum with the widget. The Number of colors can be adjusted and picked by clicking on the boxes.
To bring the whole of the tree, while keeping the style settings, into the current browser frame, use the Fit screen button (bottom right button) To automatically display the tree with collapsed nodes and fit into the frame, use the Optimise view button (bottom right button). It will autocollapse the tree and fit it into the current browser frame. In order to make labels readeable at any zoom level we are using two techniques: subsampling and screen space scaling. The first allows to display only a subset of the labels to prevent text overlap, while the second one allows to scale the labels according to the screen size. The subsampling is done by default, but you can turn it off in the settings. The screen space scaling is done automatically, and you can adjust the size of the labels using the settings. These two techniques can be computationally expensive due to the number of labels and rendering frame rate during zooming, so we remove it by default for large trees. Nevertheless, a button is available in the bottom right corner for large trees to trigger it manually.
To compare two trees, you can load them in the same session. The trees will be displayed side by side, and you can visualize topology differences with a branches color coding. You can also compute distance metrics between the two trees. Phylo.io provides several distance metrics, including Robinson-Foulds and symmetric differences. These metrics can help you quantify the differences between the two trees.
To save a phylo.io session (this contains all trees with their modifications, both viewer if in compare mode), you can use the "Save" button in the left sidebar. This will save the current state of the tree, including any modifications you have made. You can switch between trees by clicking on the tree name in the upper left corner. This will allow you to view and edit different trees within the same session. You can share a session by clicking on the "Share" button in the upper right corner. This will generate a unique URL that you can share with others, allowing them to view and edit the same session. You can export a tree by clicking on the "Download" button in the upper right corner. This will allow you to save the tree in various formats, including SVG, PNG, and PDF.
The Phylo Stack is a specialized viewer for visualizing and analyzing the evolutionary history of genes or events. It allows you to explore the distribution of genes across different taxa and understand their evolutionary relationships. The Phylo Stack provides a stacked view of the data, making it easier to identify patterns and trends in gene evolution.