<head><title>Input/Ouput</title></head>\r
<body>\r
<p><strong>Input</strong></p>\r
-<p>Jalview can read alignment files in any of the following formats:</p>\r
-<p><em>Fasta , MSF, Clustal, BLC, PIR, MSP, PFAM </em></p>\r
-<p>Use the menu at the top of the main application window to read in files from\r
-</p>\r
+<p>Jalview can read alignment files in any of the following standard formats:</p>\r
+<p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm</em></p>\r
+<p>The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a> of \r
+ these file formats.</p>\r
+<p>Additionally annotated alignments can be read in from the Jalview format. </p>\r
+<p>Use the "Input Alignment" menu at the top of the main application \r
+ window to read in files from </p>\r
<ul>\r
<li> the local file system</li>\r
- <li>a remote website</li>\r
+ <li>a website URL</li>\r
<li>or by copying and pasting into the "Cut & Paste" text window</li>\r
</ul>\r
<p>If a file is of an unknown format or there is any other error reading the alignment\r
file you will be given an error message, the alignment will not be read in.\r
</p>\r
<p><strong>Output</strong> </p>\r
-<p>Each alignment, whether it is the original or an edited version may be saved\r
- in the formats</p>\r
-<p><em>Fasta , MSF, Clustal, BLC, PIR, MSP, PFAM </em></p>\r
+<p>Each alignment, whether it is the original or an edited version may be saved \r
+ in the standard formats</p>\r
+<p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm</em></p>\r
+<p>You may save annotated alignments in the Jalview file format. </p>\r
+<p> </p>\r
+<p><strong>Export<a name="export"></a></strong></p>\r
<p>The alignment may also be saved as a HTML web page. </p>\r
<p>You may save a Portable Networks Graphics (PNG) image of your alignment. </p>\r
-<p>You may save the alignment as an Encapsulated Postscript file. This file can \r
- be easily imported into Microsoft Powerpoint, Microsoft Word or Adobe Illustrator.<br>\r
+<p>You may save the alignment as an Encapsulated Postscript file. This is a vector \r
+ graphics file which may be modified in various graphics applications, such as \r
+ Adobe Illustrator.<br>\r
+ <br>\r
Tip: When importing to a Microsoft document, a snapshot image is taken of your \r
file - this will be blurred. Right-click the image and choose "Edit image." \r
- This will restore the high quality EPS file format output. </p>\r
+ This will restore the high quality EPS file format output. <br>\r
+ NB. Mac OSX users will find that eps files are automatically converted into \r
+ PDF files. </p>\r
<p>The alignment can be printed from a local printer.</p>\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / commitdiff