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.
-+
+ 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).
+