Input

Jalview can read alignment files in any of the following formats:

Fasta , MSF, Clustal, BLC, PIR, MSP, PFAM

Use the menu at the top of the main application window to read in files from

• the local file system
• a remote website
• or by copying and pasting into the "Cut & Paste" text window

If a file is of an unknown format or there is any other error reading the alignment file you will be given an error message, the alignment will not be read in.

Output

Each alignment, whether it is the original or an edited version may be saved in the formats

Fasta , MSF, Clustal, BLC, PIR, MSP, PFAM

The alignment may also be saved as a HTML web page.

You may save a Portable Networks Graphics (PNG) image of your alignment.

You may save the alignment as an Encapsulated Postscript file. This file can be easily imported into Microsoft Powerpoint, Microsoft Word or Adobe Illustrator.
Tip: When importing to a Microsoft document, a snapshot image is taken of your file - this will be blurred. Right-click the image and choose "Edit image." This will restore the high quality EPS file format output.

The alignment can be printed from a local printer.