Exporting alignments as graphics and lineart

The alignment view can be printed using File→Print, or exported in a number of ways via the File→Export menu:

- HTML
  for viewing in a web browser
- PNG - a Portable Networks Graphics image
  For low quality diagrams and powerpoint presentations
- EPS - an Encapsulated Postscript Document
  For high quality diagrams and publications.
- SVG - a Scalable Vector Graphics document
  For high quality diagrams in publications and on the web.
- BioJS MSA - A JavaScript based multiple sequence alignment viewer.
  For interactive alignment data visualisation in a web browser.
  Get more info about the BioJS MSA viewer at http://msa.biojs.net/

Exporting alignments as Web Pages

In Jalview 2.9, new HTML exporting options were introduced. The standard HTML export option displays alignments as SVG documents embedded as scrollable panes. Exported pages can optionally also include BioJSON data, which allows Jalview to extract the original data used to create the page. Jalview can also generate HTML pages which embed BioJSON data and the BioJS MSA viewer, a pure javascript alignment viewer that provides a range of interactive analysis capabilities.

Tips for working with EPS Files

- The EPS file generated by Jalview contains vector graphics which are directly editable in graphics applications such as Adobe Illustrator.
- EPS files can be produced as "Text" or "Lineart". Use "Text" if you want the final document to be MUCH smaller in diskspace and be able to search, edit and select text. Use "Lineart" if you want an exact image of the alignment as displayed in Jalview. This is useful if a 3rd Party EPS viewer does not have the same Font which the EPS file was created with.
- When importing an EPS file into a Microsoft office document, a snapshot image of the file will be displayed which often looks blurred. Right-click the image and choose "Edit image." to convert it to word drawing objects which give a truer WYSIWIG representation.
- EPS does not support colour transparency, so will not reproduce this if used for feature colouring.
- Mac OSX users will find that eps files are automatically converted into PDF files.