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JavaScript library for developing applications and interactive visualizations involving [phylogenetic trees](https://en.wikipedia.org/wiki/Phylogenetic_tree), written as an extension of the [D3](http://d3js.org) [hierarchy layout](https://github.com/d3/","maintainers":[{"name":"maximumsteve","email":"sweaver@temple.edu"},{"name":"spond","email":"spond@temple.edu"},{"name":"dcallan","email":"dmleake92@gmail.com"}],"readme":"# phylotree.js\n\nA JavaScript library for developing applications and interactive visualizations involving [phylogenetic trees](https://en.wikipedia.org/wiki/Phylogenetic_tree), written as an extension of the [D3](http://d3js.org) [hierarchy layout](https://github.com/d3/d3-3.x-api-reference/blob/master/Hierarchy-Layout.md). It generates high quality SVG vector graphics, allows a great degree of customizability (CSS or JavaScript callbacks), and comes with a lot of *built-in* convenience features. \n\n## Quick Start\n\n### Installation\n\n```bash\nnpm install phylotree\n```\n\n### Basic Usage\n\n```javascript\nimport { phylotree } from \"phylotree\";\n\n// Parse a Newick string\nconst newick = \"((A:0.1,B:0.2):0.3,(C:0.4,D:0.5):0.6);\";\nconst tree = new phylotree(newick);\n\n// Render to an SVG container\nconst renderer = tree.render({\n  container: \"#tree-container\",\n  width: 800,\n  height: 600,\n  \"align-tips\": true,\n  zoom: true\n});\n```\n\n### TypeScript Support\n\nphylotree.js includes TypeScript declarations. Import types alongside the main export:\n\n```typescript\nimport { phylotree, PhylotreeNode, RenderOptions } from \"phylotree\";\n```\n\n## Standalone Web Application\n\nA [full-featured web application](http://phylotree.hyphy.org) based on phylotree.js, implemented in [index.html](index.html).\n\n## Features\n\n* Capable of handling multiple selection categories for comparative analysis.\n* Several mechanisms for selecting branches, including by clade, path to root, individual branches, internal branches, leaves, and branches that are nearby after layout.\n* Runs entirely in the browser, including Newick/PhyloXML/NexML parsing. \n* Can handle trees with thousands of tips.\n* Supports linear, radial, scaled branch, tip-aligned, and scaled tip size views.\n* The viewer can be constrained to fit in a given SVG box, or scale based on the size of the tree.\n* Numerous interactive features, including\n   * Scaling \n   * Animated rerooting\n   * Ladderization\n   * Clade collapse and hiding to explore large trees\n   * Node, clade, and subtree selection\n   * Tools to automatically select subsets of tree branches based on conditions.\n* Style customizations based on CSS and JavaScript callbacks\n   * Color branches and tips, including gradient shading for continuous traits. \n   * Customize the way tip names are displayed\n   * Transform branch lengths based on branch attributes (e.g. a non-linear scale).\n   * Redefine the way a tree is displayed by writing custom CSS\n* Available on [npm](https://www.npmjs.com/package/phylotree) to facilitate modern JavaScript development.\n\n## Installation\n\nIf you use NPM, `npm install phylotree`. Otherwise, the latest release can be\ninstalled locally using the following commands.\n\n```\ngit clone https://github.com/veg/phylotree.js.git\nyarn\nyarn serve\n```\n\nThis will run `rollup` in watch mode and start a local server (default port is 8080). Refresh upon editing to view changes.\n\n## Fundamentals\n\nThis section describes basic commands for displaying trees, such as those found\nin the Introduction section.\n\nNote that many methods follow the getter/setter pattern, commonly used in D3.\nThat is, they can either be used to retrieve an underlying parameter by being\ninvoked without arguments (get), or can be used to change an underlying\nparameter by being invoked with the proper arguments (set).\n\n### Supported Formats\nPhylotree supports the Newick format, as well the extension of this format that\nis used by HyPhy. This allows assigning a category to each branch by the use of\ncurly braces directly after identifiers, e.g.:\n\n```\n((((Pig:0.147969,Cow:0.21343):0.085099,Horse:0.165787,Cat:0.264806):0.058611, ((RhMonkey{Foreground}:0.002015,Baboon{Foreground}:0.003108){Foreground}:0.022733 ,(Human{Foreground}:0.004349,Chimp{Foreground}:0.000799){Foreground}:0.011873):0.101856) :0.340802,Rat:0.050958,Mouse:0.09795)\n```\n\n## Examples\n\n### Observable Notebooks\n* [Simple Example](https://observablehq.com/@stevenweaver/phylotree-1-0-0?collection=@stevenweaver/phylotree-utilities)\n* [Unscaled IAV HA colored by host](https://observablehq.com/@stevenweaver/phylotree-1-0-0-unscaled-iav-ha-colored-by-host?collection=@stevenweaver/phylotree-utilities)\n* [HIV RT](https://observablehq.com/@stevenweaver/phylotree-1-0-0-hiv-rt?collection=@stevenweaver/phylotree-utilities)\n* [NGS Copy Diversity](https://observablehq.com/@stevenweaver/ngs-copy-diversity-with-phylotree-1-0-0?collection=@stevenweaver/phylotree-utilities)\n* [HIV-1 env multiple timepoints and compartments](https://observablehq.com/@stevenweaver/hiv-1-env-multiple-timepoints-and-compartments-with-phylot?collection=@stevenweaver/phylotree-utilities)\n* [Computing Root-to-Tip Distances with Phylotree.js](https://observablehq.com/@stevenweaver/computing-root-to-tip-distances-with-phylotree-js?collection=@stevenweaver/phylotree-utilities)\n* [Computing the Center of the Tree with Phylotree.js](https://observablehq.com/@stevenweaver/computing-the-center-of-the-tree-with-phylotree-js?collection=@stevenweaver/phylotree-utilities)\n* [Identifying Clusters in a Phylogenetic Tree with Phylotree.js](https://observablehq.com/@stevenweaver/identifying-clusters-in-a-phylogenetic-tree-with-phylotre?collection=@stevenweaver/phylotree-utilities)\n* [Identifying Clusters in a Phylogenetic Tree with Phylotree.js Part II](https://observablehq.com/@stevenweaver/identifying-clusters-in-a-phylogenetic-tree-with-phylotre/2?collection=@stevenweaver/phylotree-utilities)\n\n📚 View the complete [Observable Collection](https://observablehq.com/collection/@stevenweaver/phylotree-utilities)\n\n## Utility Functions\n\nphylotree.js exports several utility functions for phylogenetic analysis:\n\n### Tree Metrics\n\n```javascript\nimport {\n  pairwiseDistances,  // Compute pairwise distances between nodes\n  sackin,             // Sackin's index (tree balance measure)\n  centerOfTree,       // Find the center node of the tree\n  computeMidpoint,    // Compute midpoint for rooting\n  rootToTip,          // Root-to-tip distance regression\n  fitRootToTip        // Find optimal root by R² maximization\n} from \"phylotree\";\n```\n\n### Clustering Algorithms\n\n```javascript\nimport {\n  clusterPicker,  // Cluster Picker algorithm for transmission cluster identification\n  phylopart       // PhyloPart clustering algorithm\n} from \"phylotree\";\n\n// Example: Identify clusters\nconst clusters = clusterPicker(tree, {\n  bootstrap_threshold: 0.9,\n  distance_threshold: 0.045\n});\n```\n\n### Tree Construction\n\n```javascript\nimport {\n  neighborJoining,    // Build tree from distance matrix\n  getDistanceMatrix,  // Compute distance matrix from sequences\n  parseFasta          // Parse FASTA format sequences\n} from \"phylotree\";\n\n// Example: Build tree from sequences\nconst sequences = parseFasta(fastaString);\nconst { matrix, labels } = getDistanceMatrix(sequences);\nconst treeJson = neighborJoining(matrix, labels);\n```\n\n### Parsers and Export\n\n```javascript\nimport {\n  newickParser,      // Parse Newick format strings\n  getNewick,         // Export tree to Newick format\n  loadAnnotations,   // Load annotations from NEXUS files\n  extractDates       // Extract dates from tip names\n} from \"phylotree\";\n```\n\n## Options\n\nphylotree.js supports a variety of options for common features, which can be set using\nthe following function.\n\nThe following are a list of possible options, along with their types, meanings, and possible values.\n\n### left-right-spacing\n  `(String)` Determines layout size from left to right. Defaults to ``\"fixed-step\"``.\n\n  * ``\"fixed-step\"`` - Determine width from padding and spacing.\n  * ``\"fit-to-size\"`` - Determine width from size array.\n\n### top-bottom-spacing\n  `(String)` Determines layout size from top to bottom. Defaults to ``\"fixed-step\"``.\n\n  * ``\"fixed-step\"`` - Determine width from padding and spacing.\n  * ``\"fit-to-size\"`` - Determine width from size array.\n\n### brush\n  `(Boolean)` Whether or not the brush should be activated. Defaults to ``true``.\n\n### hide\n  `(Boolean)` Whether or not hiding a given node or subtree is enabled. Defaults to ``true``.\n\n### reroot\n  `(Boolean)` Whether or not rerooting on a given node is enabled. Defaults to ``true``.\n\n### compression\n  `(Number)` The percentage of original size for a collapsed node. Defaults to ``.2``.\n\n### show-scale\n  `(Boolean)` Determines whether or not scale bar for branch lengths is shown.\n\n### left-offset\n  `(Number)` Amount of space on left side of phylotree. Defaults to ``0``.\n\n### draw-size-bubbles\n  `(Boolean)` Determines whether nodes are drawn with a given size. Defaults to ``false``.\n\n### max-radius\n  `(Number)` Set an upper bound on the radius in a radial layout. Defaults to 768.\n\n### collapsible\n  `(Boolean)` Determines whether or not nodes are collapsible. Defaults to ``true``.\n\n### selectable\n  `(Boolean)` Determines whether or not individual branches are selectable. Defaults to ``true``.\n\n### zoom\n  `(Boolean)` Determines whether or not zooming is enabled. Defaults to ``false``.\n\n### restricted-selectable\n  `(Array)` Determines what types of global selection actions are possible. Defaults to ``false``.\n\n  * ``false`` - No restrictions placed on global selection.\n  * ``\"all\"`` - Allow users to select all branches.\n  * ``\"none\"`` - Allow users to unselect all branches.\n  * ``\"all-leaf-nodes\"`` - Allow users to select all leaf nodes.\n  * ``\"all-internal-branches\"`` - Allow users to select all internal branches.\n\n### align-tips\n  `(Boolean)` Determines whether tip names are aligned or not. Defaults to false.\n\n### maximum-per-node-spacing\n  `(Number)` Determines maximum node spacing allocated when laying out left to right. Defaults to 100.\n\n### minimum-per-node-spacing\n  `(Number)` Determines minimum node spacing allocated when laying out left to right. Defaults to 2.\n\n### maximum-per-level-spacing\n  `(Number)` Determines maximum node spacing allocated when laying out top to bottom. Defaults to 100.\n\n### minimum-per-level-spacing\n  `(Number)` Determines minimum node spacing allocated when laying out top to bottom. Defaults to 10.\n\n## API Reference\nA complete list of available functions can be found at [API.md](API.md)\n\n","readmeFilename":"README.md"}