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 jpg image of your alignment.

The alignment can be printed from a local printer.