X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fio%2Findex.html;h=d57de42e7adf719280f2be9a9fd8b98bb128cf33;hb=74fee91ef567d4637911a9c20834c9fb1de8c64a;hp=c7c4bf8a042527210e9b7c02b0ba0bc850d08458;hpb=ff761b8bfedf4dde4672eaed9e51bbf71bfe207e;p=jalview.git diff --git a/help/html/io/index.html b/help/html/io/index.html index c7c4bf8..d57de42 100755 --- a/help/html/io/index.html +++ b/help/html/io/index.html @@ -1,30 +1,48 @@ -
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 (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.
+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.
+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 formats
-Fasta , MSF, Clustal, BLC, PIR, MSP, PFAM
-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 file can
- be easily imported into Microsoft Powerpoint, Microsoft Word or 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.
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
+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.
+