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
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.
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.