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 alignments can be read in from the Jalview format.
-Use the "Input Alignment" menu at the top of the main application - window 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. -
-Output
-Each alignment, whether it is the original or an edited version may be saved - in the standard formats
-Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm
-You may save annotated alignments in the Jalview file format.
-- -
The alignment may also be saved as a HTML web page.
-You may save a Portable Networks Graphics (PNG) image of your alignment.
-You may save the alignment as an Encapsulated Postscript file. This is a vector
- graphics file which may be modified in various graphics applications, such as
- Adobe Illustrator.
-
- Tip: When importing to a Microsoft document, a snapshot image is taken of your
- file - this will be blurred. Right-click the image and choose "Edit image."
- This will restore the high quality EPS file format output.
- NB. Mac OSX users will find that eps files are automatically converted into
- PDF files.
The alignment can be printed from a local printer.
- - + + + ++ 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 +
++ 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.
The project data includes the state of any open
+ structure viewers (Jmol, and since Jalview 2.9 also Chimera
+ and Varna).
+
+ +