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 -
+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:
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. +
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 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.
+ in the standard formats using File→Save As +Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm
+You can also save the current set of alignments and their colours, annotations and +trees in a Jalview archive file using Desktop→Save project.
+