Input

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

Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm

The EBI has examples of these file formats.

Additionally annotated alignments can be read in from the Jalview format.

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

• the local file system
• a website URL
• 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 standard formats

Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm

You may save annotated alignments in the Jalview file format.

Export

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 is a vector graphics file which may be modified in various graphics applications, such as 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.
NB. Mac OSX users will find that eps files are automatically converted into PDF files.

The alignment can be printed from a local printer.