phylotree

Description
This extension provides a simple file formatter for newick tree files using the library phylotree¹ for display.


1: Shank et al., phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics, BMC Bioinformatics (07/2018), https://doi.org/10.1186/s12859-018-2283-2


Installation

• Install as you would normally install a contributed Drupal module. See:
  https://drupal.org/documentation/install/modules-themes/modules-7
  for further information.
• Install the d3.js v3 library:
  download https://github.com/d3/d3/releases/download/v3.5.17/d3.zip
  and extract it to a d3js3 directory in your library directory (so
  you should have: .../sites/XXX/libraries/d3js3/d3.min.js).
• Install the bootstrap v3 library:
  download
  https://github.com/twbs/bootstrap/releases/download/v3.3.7/bootstrap-3.3...
  and extract it to a bootstrap directory in your library directory (so
  you should have: .../sites/XXX/libraries/bootstrap/bootstrap.min.js).
• Install the underscore v1 library:
  download https://underscorejs.org/underscore-min.js
  and extract it to an underscore directory in your library directory (so
  you should have: .../sites/XXX/libraries/underscore/underscore-min.js).
• Install the fontawesome v4 library:
  download https://fontawesome.com/v4.7.0/#modal-download
  and extract it to a fontawesome directory in your library directory (so
  you should have:
  .../sites/XXX/libraries/fontawesome/css/font-awesome.min.css).
• Enable the module in "Admin menu > Site building > Modules" (path
  /admin/modules).

Use

• Create or use an existing content type.
• Add a "file" field to that content type (admin/structure/types --> manage fields) and filter extensions to "nwk,newick,nhx" (for instance).
• Change the formatter of that file (manage display) to use "Phylotree".
• Create a corresponding content with a newick file and display it.

note: this formatter can also be used in views or other places and it supports
multiple trees on a same page.