Jalview can read alignment files in any of the following standard formats:
Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR (including MODELLER variant), Pfam/Stockholm
The EBI has examples of these file formats.
Additionally, whole sets of coloured and annotated alignments and trees can be read from a Jalview (jar) format file using Desktop→Load Project.
Press "Control O" to open a file browser, or use the Desktop→Input Alignment menu to read in alignments from:
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 email@example.com.
Jalview can also read jalview specific files for sequence features and alignment annotation.
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/StockholmJalview 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. In the case of PIR format, the output tab also contains a switch for turning on the output of Modeller style structured description lines.
Quantitative and symbolic alignment annotation can be exported as a comma separated value file by right clicking on an annotation row under the alignment.
You can also save the current set of alignments and their colours, annotations and trees in a Jalview archive file using Desktop→Save project.