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
+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, annotated whole sets of alignments and trees can be -read from a Jalview -(jar) format file using Desktop→Load Project.
+read from a Jalview (jar) +format file using Desktop→Load +Project.Use the Desktop→Input Alignment menu to read in files from:
Jalview can also read jalview specific files for sequence features +and alignment annotation.
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. 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.