<body>\r
<p><strong>Input</strong></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><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file,\r
+NBRF/PIR (including MODELLER variant), 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 whole sets of alignments and trees can be\r
in the format /start-end. If you do not want this behaviour for a particular file \r
output, open the "Output" tab on the <a href="../features/preferences.html">Preferences</a> window where you can \r
select which file formats you want to append the start and end sequence positions \r
-for.\r
+for. In the case of PIR format, the output tab also contains a switch\r
+for turning on the output of Modeller style structured description\r
+lines.\r
<p>Quantitative and symbolic <a href="../features/annotation.html">alignment annotation</a> can be exported as a\r
comma separated value file by right clicking on an annotation row\r
under the alignment.</p>\r
git://source.jalview.org / jalview.git / commitdiff