Exporting alignments as artwork

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/

PNG Export Options

Since Jalview 2.11.3 it is possible to specify options when exporting figures via the command line to increase the resolution of the exported PNG, and configure maximum width and height settings.

You can also configure default export settings by adding the following lines to

.jalview_properties

BITMAP_SCALE=<Scale factor multiplied by 10>
  BITMAP_WIDTH=Width of export in pixels
  BITMAP_HEIGHT=Height of figure export in pixels

When scale is not set, the figure will be scaled to fit in the smallest specified dimension. Scale will be ignored if it results in an image dimension greater than the smallest specified dimension.

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.