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2.1 updates
[jalview.git]
/
help
/
html
/
io
/
index.html
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help/html/io/index.html
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<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>
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+<p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file,
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+NBRF/PIR (including MODELLER variant), Pfam/Stockholm</em></p>
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<p>The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a> of
\r
these file formats.</p>
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<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
@@
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+35,9
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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
\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
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.
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<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>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