Input
+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 help@jalview.org.
+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.
++ +