Input/Output

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 whole sets of alignments and trees can be read from a Jalview (jar) format file using Desktop→Load Project.

Use the Desktop→Input Alignment menu to read in files from:

From File: the local file system
From URL: the web (please use the full url)
from Textbox: a copy and paste into the "Cut & Paste" text window

Jalview will try to recognise the file type automatically (using some special features). If a file is of an unknown format or there is any other error reading the alignment file then you will be given an error message. If you think Jalview really should be able to read your file, then send an email containing the problem file to jalview@jalview.org.

Output

Each alignment, whether it is the original or an edited version may be saved in the standard formats using File→Save As

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

Jalview will by default append the sequence start and end to each sequence name, in the format /start-end. If you do not want this behaviour for a particular file output, open the "Output" tab on the Preferences window where you can select which file formats you want to append the start and end sequence positions for.

You can also save the current set of alignments and their colours, annotations and trees in a Jalview archive file using Desktop→Save project.