<body>\r
<p><strong>Input</strong></p>\r
<p>Jalview can read alignment files in any of the following standard formats:</p>\r
<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
<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
Jalview really should be able to read your file, then send an email\r
containing the problem file to jalview@jalview.org.\r
</p>\r
Jalview really should be able to read your file, then send an email\r
containing the problem file to jalview@jalview.org.\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 standard formats using <strong>File→Save As</strong></p>\r
<p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm</em></p>\r
Jalview will by default append the sequence start and end to each sequence name, \r
in the format /start-end. If you do not want this behaviour for a particular file \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 standard formats using <strong>File→Save As</strong></p>\r
<p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm</em></p>\r
Jalview will by default append the sequence start and end to each sequence name, \r
in the format /start-end. If you do not want this behaviour for a particular file \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
<p>You can also save the current set of alignments and their colours, annotations and\r
trees in a Jalview archive file using <strong>Desktop→Save project</strong>. </p>\r
<p> </p>\r
<p>You can also save the current set of alignments and their colours, annotations and\r
trees in a Jalview archive file using <strong>Desktop→Save project</strong>. </p>\r
<p> </p>\r