<body>\r
<p><strong>Alignment Window Menus</strong></p>\r
<ul>\r
- <li><strong>File</strong>\r
+ <li><strong>File</strong> \r
<ul>\r
+ <li><strong>Add Sequences</strong><em><br>\r
+ Add sequences to the visible alignment from file, URL, or cut & paste \r
+ window </em></li>\r
<li><strong>Fetch Sequence</strong><br>\r
- <em>Shows a dialog window in which you can select known ids from Uniprot,\r
- EMBL, EMBLCDS or PDB database using Web Services provided by the European\r
- Bioinformatics Institute. See <a href="../features/seqfetch.html">Sequence\r
+ <em>Shows a dialog window in which you can select known ids from Uniprot, \r
+ EMBL, EMBLCDS or PDB database using Web Services provided by the European \r
+ Bioinformatics Institute. See <a href="../features/seqfetch.html">Sequence \r
Fetcher</a></em>.</li>\r
<li><strong>Save As<br>\r
- </strong><em>Save the alignment to local file. A file selection window\r
- will open, use the "Files of type:" selection box to determine\r
+ </strong><em>Save the alignment to local file. A file selection window \r
+ will open, use the "Files of type:" selection box to determine \r
which <a href="../io/index.html">alignment format</a> to save as.</em></li>\r
<li><strong>Export</strong> <em><br>\r
- Creates an alignment graphic with the current annotation, alignment background\r
+ Creates an alignment graphic with the current annotation, alignment background \r
colours and group colours. If the alignment is <a\r
- href="../features/wrap.html">wrapped</a>, the output will also be wrapped\r
- and will have the same visible residue width as the open alignment. </em>\r
+ href="../features/wrap.html">wrapped</a>, the output will also be wrapped \r
+ and will have the same visible residue width as the open alignment. </em> \r
<ul>\r
<li><strong>HTML<br>\r
- </strong><em>Create a <a href="../io/export.html">web page</a>\r
- from your alignment.</em></li>\r
+ </strong><em>Create a <a href="../io/export.html">web page</a> from \r
+ your alignment.</em></li>\r
<li><strong>EPS<br>\r
- </strong><em>Create an <a href="../io/export.html">Encapsulated\r
- Postscript</a> file from your alignment.</em></li>\r
+ </strong><em>Create an <a href="../io/export.html">Encapsulated Postscript</a> \r
+ file from your alignment.</em></li>\r
<li><strong>PNG<br>\r
- </strong><em>Create a <a href="../io/export.html">Portable Network\r
+ </strong><em>Create a <a href="../io/export.html">Portable Network \r
Graphics</a> file from your alignment.</em></li>\r
</ul>\r
</li>\r
<li><strong>Output to Textbox<br>\r
- </strong><em>The alignment will be displayed in plain text in a new window\r
- which you can "Copy and Paste" using the pull down menu, or\r
+ </strong><em>The alignment will be displayed in plain text in a new window \r
+ which you can "Copy and Paste" using the pull down menu, or \r
your standard operating system copy and paste keys. <br>\r
- Select the format of the text by selecting one of the following menu items.</em>\r
+ Select the format of the text by selecting one of the following menu items.</em> \r
<ul>\r
<li><strong>FASTA</strong> <em></em></li>\r
<li><strong>MSF</strong></li>\r
</ul>\r
</li>\r
<li><strong>Print<br>\r
- </strong><em>Jalview will print the alignment using the current fonts\r
- and colours of your alignment. If the alignment has annotations visible,\r
- these will be printed below the alignment. If the alignment is wrapped\r
- the number of residues per line of your alignment will depend on the paper\r
+ </strong><em>Jalview will print the alignment using the current fonts \r
+ and colours of your alignment. If the alignment has annotations visible, \r
+ these will be printed below the alignment. If the alignment is wrapped \r
+ the number of residues per line of your alignment will depend on the paper \r
width or your alignment window width, whichever is the smaller. </em></li>\r
+ <li><strong>Export Features</strong><em><br>\r
+ All features visible on the alignment can be saved to file or displayed \r
+ in a textbox in either Jalview or GFF format</em></li>\r
+ <li><strong>Export Annotations</strong><em><br>\r
+ All annotations visible on the alignment can be saved to file or displayed \r
+ in a textbox in Jalview annotations format. </em></li>\r
<li><strong>Load Associated Tree<br>\r
</strong><em>Jalview can <a\r
- href="../calculations/treeviewer.html">view trees</a> stored in the Newick\r
- file format, and associate them with the alignment. Note: the ids of the\r
+ href="../calculations/treeviewer.html">view trees</a> stored in the Newick \r
+ file format, and associate them with the alignment. Note: the ids of the \r
tree file and your alignment MUST be the same.</em></li>\r
<li><strong>Load Features / Annotations<br>\r
- </strong><em>Load files describing precalculated <a href="../features/featuresFormat.html">sequence\r
- features</a> or <a href="../features/annotationsFormat.html">alignment\r
+ </strong><em>Load files describing precalculated <a href="../features/featuresFormat.html">sequence \r
+ features</a> or <a href="../features/annotationsFormat.html">alignment \r
annotations</a>.</em></li>\r
- <li><strong>Close<br>\r
- </strong><em>Close the alignment window. Make sure you have saved your\r
- alignment before you close - either as a Jalview project or by using the\r
- <strong>Save As</strong> menu.<br>\r
+ <li><strong>Close</strong><br>\r
+ <em>Close the alignment window. Make sure you have saved your alignment \r
+ before you close - either as a Jalview project or by using the <strong>Save \r
+ As</strong> menu.<br>\r
</em></li>\r
</ul>\r
</li>\r
- <li><strong>Edit</strong>\r
+ <li><strong>Edit</strong> \r
<ul>\r
<li><strong>Undo</strong><em><br>\r
- This will undo any edits you make to the alignment. This applies to insertion\r
- or deletion of gaps, cutting residues or sequences from the alignment\r
- or pasting sequences to the current alignment or sorting the alignment.\r
- <strong>NOTE:</strong> It DOES NOT undo colour changes, adjustments to\r
+ This will undo any edits you make to the alignment. This applies to insertion \r
+ or deletion of gaps, cutting residues or sequences from the alignment \r
+ or pasting sequences to the current alignment or sorting the alignment. \r
+ <strong>NOTE:</strong> It DOES NOT undo colour changes, adjustments to \r
group sizes, or changes to the annotation panel. </em></li>\r
<li><strong>Redo<br>\r
</strong><em>Any actions which you undo can be redone using redo. </em></li>\r
<li><strong>Cut<br>\r
- </strong><em>This will make a copy of the currently selected residues\r
- before removing them from your alignment. Click on a sequence name if\r
+ </strong><em>This will make a copy of the currently selected residues \r
+ before removing them from your alignment. Click on a sequence name if \r
you wish to select a whole sequence. <br>\r
Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>\r
<li><strong>Copy</strong><br>\r
- <em>Copies the currently selected residues to the system clipboard - you\r
- can also do this by pressing <CTRL> and C (<APPLE> and C on\r
+ <em>Copies the currently selected residues to the system clipboard - you \r
+ can also do this by pressing <CTRL> and C (<APPLE> and C on \r
MacOSX). <br>\r
- If you try to paste the clipboard contents to a text editor, you will\r
+ If you try to paste the clipboard contents to a text editor, you will \r
see the format of the copied residues FASTA.</em></li>\r
- <li><strong>Paste </strong>\r
+ <li><strong>Paste </strong> \r
<ul>\r
<li><strong>To New Alignment<br>\r
- </strong><em>A new alignment window will be created from sequences\r
+ </strong><em>A new alignment window will be created from sequences \r
previously copied or cut to the system clipboard. <br>\r
Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.</em></li>\r
<li><strong>Add To This Alignment<br>\r
- </strong><em>Copied sequences from another alignment window can be\r
+ </strong><em>Copied sequences from another alignment window can be \r
added to the current Jalview alignment. </em></li>\r
</ul>\r
</li>\r
<li><strong>Delete<br>\r
- </strong><em>This will delete the currently selected residues without\r
- copying them to the clipboard. Like the other edit operations, this can\r
+ </strong><em>This will delete the currently selected residues without \r
+ copying them to the clipboard. Like the other edit operations, this can \r
be undone with <strong>Undo</strong>.</em></li>\r
<li><strong>Select All<br>\r
- </strong><em>Selects all the sequences and residues in the alignment.\r
+ </strong><em>Selects all the sequences and residues in the alignment. \r
<br>\r
Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.</em></li>\r
<li><strong>Deselect All<br>\r
- </strong><em>Removes the current selection box (red dashed box) from the\r
- alignment window. All selected sequences, residues and marked columns\r
+ </strong><em>Removes the current selection box (red dashed box) from the \r
+ alignment window. All selected sequences, residues and marked columns \r
will be deselected. </em><em> <br>\r
Use <ESCAPE> to deselect all.</em></li>\r
- <li><strong>Invert Selection<br>\r
- </strong><em>Any sequence ids currently not selected will replace the\r
+ <li><strong>Invert Sequence Selection<br>\r
+ </strong><em>Any sequence ids currently not selected will replace the \r
current selection. </em></li>\r
+ <li><strong>Invert Column Selection<br>\r
+ </strong><em>Any columns currently not selected will replace the current \r
+ column selection. </em></li>\r
<li><strong>Undefine Groups<br>\r
</strong><em>The alignment will be reset with no defined groups.<br>\r
<strong>WARNING</strong>: This cannot be undone.</em></li>\r
<li><strong>Remove Left<br>\r
- </strong><em>If the alignment has marked columns, the alignment will be\r
- trimmed to the left of the leftmost marked column. To mark a column, mouse\r
- click the scale bar above the alignment. Click again to unmark a column,\r
+ </strong><em>If the alignment has marked columns, the alignment will be \r
+ trimmed to the left of the leftmost marked column. To mark a column, mouse \r
+ click the scale bar above the alignment. Click again to unmark a column, \r
or select "Deselect All" to deselect all columns.</em></li>\r
<li><strong>Remove Right<br>\r
- </strong><em>If the alignment has marked columns, the alignment will be\r
- trimmed to the left of the leftmost marked column. To mark a column, mouse\r
- click the scale bar above the alignment. Click again to unmark a column,\r
+ </strong><em>If the alignment has marked columns, the alignment will be \r
+ trimmed to the left of the leftmost marked column. To mark a column, mouse \r
+ click the scale bar above the alignment. Click again to unmark a column, \r
or select "Deselect All" to deselect all columns.</em></li>\r
<li><strong>Remove Empty Columns<br>\r
- </strong><em>All columns which only contain gap characters ("-",\r
+ </strong><em>All columns which only contain gap characters ("-", \r
".") will be deleted.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
+ You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
</em></li>\r
<li><strong>Remove All Gaps</strong><br>\r
- <em>Gap characters ("-", ".") will be deleted from\r
- the selected area of the alignment. If no selection is made, ALL the gaps\r
+ <em>Gap characters ("-", ".") will be deleted from \r
+ the selected area of the alignment. If no selection is made, ALL the gaps \r
in the alignment will be removed.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
+ You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
</em> </li>\r
<li><strong>Remove Redundancy<br>\r
- </strong><em>Selecting this option brings up a window asking you to select\r
- a threshold. If the percentage identity between any two sequences (under\r
- the current alignment) exceeds this value then one of the sequences (the\r
- shorter) is discarded. Press the "Apply" button to remove redundant\r
+ </strong><em>Selecting this option brings up a window asking you to select \r
+ a threshold. If the percentage identity between any two sequences (under \r
+ the current alignment) exceeds this value then one of the sequences (the \r
+ shorter) is discarded. Press the "Apply" button to remove redundant \r
sequences. The "Undo" button will undo the last redundancy deletion.</em></li>\r
- <li><strong>Pad Gaps<br>\r
- </strong><em>When selected, the alignment will be kept at minimal\r
- width (so there no empty columns before or after the first or last aligned\r
- residue) and all sequences will be padded with gap characters to\r
- the before and after their terminating residues.<br>\r
- This switch is useful when making a tree using unaligned\r
- sequences and when working with alignment analysis programs which\r
- require 'properly aligned sequences' to be all the same length.<br>\r
- You may set the default for <strong>Pad Gaps</strong> in the <a href="../features/preferences.html">preferences</a>.\r
- </em></li>\r
+ <li><strong>Pad Gaps<br>\r
+ </strong><em>When selected, the alignment will be kept at minimal width \r
+ (so there no empty columns before or after the first or last aligned residue) \r
+ and all sequences will be padded with gap characters to the before and \r
+ after their terminating residues.<br>\r
+ This switch is useful when making a tree using unaligned sequences and \r
+ when working with alignment analysis programs which require 'properly \r
+ aligned sequences' to be all the same length.<br>\r
+ You may set the default for <strong>Pad Gaps</strong> in the <a href="../features/preferences.html">preferences</a>. \r
</em><br>\r
</li>\r
</ul>\r
</li>\r
- <li><strong>Search</strong>\r
+ <li><strong>Search</strong> \r
<ul>\r
<li><strong>Find<br>\r
- </strong><em>Select this to <a href="../features/search.html">search</a>\r
- for residues, sequence name or residue position within the\r
- alignment and create new sequence features from the queries.\r
- <br>\r
+ </strong><em>Select this to <a href="../features/search.html">search</a> \r
+ for residues, sequence name or residue position within the alignment and \r
+ create new sequence features from the queries. <br>\r
</em></li>\r
</ul>\r
</li>\r
- <li><strong>View</strong>\r
+ <li><strong>View</strong> \r
<ul>\r
<li><strong>Font<br>\r
- </strong><em>Change the font of the display from the "Choose Font"\r
+ </strong><em>Change the font of the display from the "Choose Font" \r
dialog box, which is shown when this item is selected. </em></li>\r
<li><strong>Smooth Fonts</strong><em><br>\r
- If selected, the alignment will be drawn with anti-aliasing on which looks\r
- better, but performace is reduced.\r
- </em></li>\r
+ If selected, the alignment will be drawn with anti-aliasing on which looks \r
+ better, but performace is reduced. </em></li>\r
+ <li><strong>Show (all Columns / Sequences)</strong><em><br>\r
+ All hidden Columns / Sequences will be revealed. </em></li>\r
+ <li><strong>Hide (all Columns / Sequences)</strong><em><br>\r
+ Hides the all the currently selected Columns / Sequences</em></li>\r
<li><strong>Wrap<br>\r
- </strong><em>When ticked, the alignment display is "<a href="../features/wrap.html">wrapped</a>"\r
- to the width of the alignment window. This is useful if your alignment\r
+ </strong><em>When ticked, the alignment display is "<a href="../features/wrap.html">wrapped</a>" \r
+ to the width of the alignment window. This is useful if your alignment \r
has only a few sequences to view its full width at once.<br>\r
- Options are available to show the residue numbering at the start and/or\r
- end of an alignment as well as showing the alignment position above each\r
+ Options are available to show the residue numbering at the start and/or \r
+ end of an alignment as well as showing the alignment position above each \r
sequence row. <br>\r
- <strong>NOTE</strong>: When in wrapped alignment view, the alignment cannot\r
+ <strong>NOTE</strong>: When in wrapped alignment view, the alignment cannot \r
be edited or have regions selected on it. </em></li>\r
<li><strong>Show Full Sequence ID<br>\r
- </strong><em>If this box is selected the sequence name will have the start\r
+ </strong><em>If this box is selected the sequence name will have the start \r
and end position of the sequence appended to the name, in the format NAME/START-END</em></li>\r
<li><strong>Boxes</strong><em><br>\r
- If this is selected the background of a residue will be coloured using\r
- the selected background colour. Useful if used in conjunction with "Colour\r
+ If this is selected the background of a residue will be coloured using \r
+ the selected background colour. Useful if used in conjunction with "Colour \r
Text." </em></li>\r
<li><strong>Text<br>\r
- </strong><em>If this is selected the residues will be displayed using\r
+ </strong><em>If this is selected the residues will be displayed using \r
the standard 1 character amino acid alphabet.</em></li>\r
<li><strong>Colour Text<br>\r
- </strong><em>If this is selected the residues will be coloured according\r
- to the background colour associated with that residue. The colour is slightly\r
+ </strong><em>If this is selected the residues will be coloured according \r
+ to the background colour associated with that residue. The colour is slightly \r
darker than background so the amino acid symbol remains visible. </em></li>\r
<li><strong>Show Gaps<br>\r
- </strong><em>When this is selected, gap characters will be displayed as\r
- "." or "-". If unselected, then gap characters will\r
+ </strong><em>When this is selected, gap characters will be displayed as \r
+ "." or "-". If unselected, then gap characters will \r
appear as blank spaces. <br>\r
You may set the default gap character in <a href="../features/preferences.html">preferences</a>.</em></li>\r
<li><strong>Show Annotations<br>\r
- </strong><em>If this is selected the "Annotation Panel" will\r
- be displayed below the alignment. The default setting is to display the\r
- conservation calculation, quality calculation and consensus values as\r
+ </strong><em>If this is selected the "Annotation Panel" will \r
+ be displayed below the alignment. The default setting is to display the \r
+ conservation calculation, quality calculation and consensus values as \r
bar charts. </em></li>\r
<li><strong>Fetch Sequence Features<br>\r
- </strong><em>If the sequence names are Swissprot entries Jalview will\r
- use the names to retrieve <a href="../features/seqfeatures.html">sequence\r
- features</a> from the EBI. Features which are 1 residue in length are\r
- coloured red, sequences longer than 1 residue are coloured blue. Move\r
- the mouse over a coloured feature to display the details of the feature.\r
+ </strong><em>If the sequence names are Swissprot entries Jalview will \r
+ use the names to retrieve <a href="../features/seqfeatures.html">sequence \r
+ features</a> from the EBI. Features which are 1 residue in length are \r
+ coloured red, sequences longer than 1 residue are coloured blue. Move \r
+ the mouse over a coloured feature to display the details of the feature. \r
<br>\r
- Note: The retrieved information will update the sequence start and end\r
+ Note: The retrieved information will update the sequence start and end \r
labels if they are incorrect. </em></li>\r
- <li><strong>Show Sequence Features</strong><br><em>Show or\r
- hide sequence features on this alignment.</em></li>\r
- <li><strong>Seqence Feature Settings...</strong><em><br>\r
- <em>Control the colour and display of sequence features on the\r
- alignment. See <a\r
- href="../features/featuresettings.html">Sequence Feature Settings</a>.</em><br>\r
- </em></li>\r
+ <li><strong>Show Sequence Features</strong><br>\r
+ <em>Show or hide sequence features on this alignment.</em></li>\r
+ <li><strong>Seqence Feature Settings...</strong><em><br>\r
+ <em>Control the colour and display of sequence features on the alignment. \r
+ See <a\r
+ href="../features/featuresettings.html">Sequence Feature Settings</a>.</em></em></li>\r
<li><strong><a href="../features/overview.html">Overview Window</a><br>\r
- </strong><em>A scaled version of the alignment will be displayed in a\r
- small window. A red box will indicate the currently visible area of the\r
+ </strong><em>A scaled version of the alignment will be displayed in a \r
+ small window. A red box will indicate the currently visible area of the \r
alignment. Move the visible region using the mouse. </em><strong> </strong></li>\r
</ul>\r
</li>\r
- <li><strong>Colour</strong>\r
+ <li><strong>Colour</strong> \r
<ul>\r
<li><strong>Apply Colour To All Groups<br>\r
- </strong><em>If this is selected, any changes made to the background colour\r
+ </strong><em>If this is selected, any changes made to the background colour \r
will be applied to all currently defined groups.</em></li>\r
- <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage\r
- Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,\r
+ <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage \r
+ Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity, \r
Turn Propensity, Buried Index, Nucleotide, User Defined<br>\r
- </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for\r
+ </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for \r
a description of all colour schemes.</em></li>\r
<li><strong>By Conservation<br>\r
- </strong><em>See <a href="../colourSchemes/conservation.html">Colouring\r
+ </strong><em>See <a href="../colourSchemes/conservation.html">Colouring \r
by Conservation</a>.</em></li>\r
<li><strong>Modify Conservation Threshold<br>\r
- </strong><em>Use this to display the conservation threshold slider window.\r
- Useful if the window has been closed, or if the 'by conservation' option\r
+ </strong><em>Use this to display the conservation threshold slider window. \r
+ Useful if the window has been closed, or if the 'by conservation' option \r
appears to be doing nothing!</em></li>\r
<li><strong>Above Identity Threshold<br>\r
- </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage\r
+ </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage \r
Identity</a></em><strong>.</strong></li>\r
<li><strong>Modify Identity Threshold<br>\r
- </strong><em>Use this to set the threshold value for colouring above Identity.\r
- Useful if the window has been closed. <br>\r
- </em></li>\r
- <li><strong>By Annotation</strong><br>\r
- <em>Colours the alignment on a per-column value from a specified annotation.\r
- See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>\r
- </li>\r
+ </strong><em>Use this to set the threshold value for colouring above Identity. \r
+ Useful if the window has been closed. </em></li>\r
+ <li><strong>By Annotation</strong><br>\r
+ <em>Colours the alignment on a per-column value from a specified annotation. \r
+ See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>\r
+ </li>\r
</ul>\r
</li>\r
- <li><strong>Calculate</strong>\r
+ <li><strong>Calculate</strong> \r
<ul>\r
- <li>Sort\r
+ <li>Sort \r
<ul>\r
<li><strong>by ID</strong><em><br>\r
- This will sort the sequences according to sequence name. If the sort\r
+ This will sort the sequences according to sequence name. If the sort \r
is repeated, the order of the sorted sequences will be inverted. </em></li>\r
<li><strong>by Group</strong><strong><br>\r
- </strong><em>This will sort the sequences according to sequence name.\r
- If the sort is repeated, the order of the sorted sequences will be\r
+ </strong><em>This will sort the sequences according to sequence name. \r
+ If the sort is repeated, the order of the sorted sequences will be \r
inverted. </em><strong></strong></li>\r
<li><strong>by Pairwise Identity<br>\r
- </strong><em>This will sort the selected sequences by their percentage\r
- identity to the consensus sequence. The most similar sequence is put\r
+ </strong><em>This will sort the selected sequences by their percentage \r
+ identity to the consensus sequence. The most similar sequence is put \r
at the top. </em></li>\r
- <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will\r
- have some additional options if you have just done a multiple alignment\r
+ <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will \r
+ have some additional options if you have just done a multiple alignment \r
calculation, or opened a tree viewer window.</em></li>\r
</ul>\r
</li>\r
<li><strong>Calculate Tree </strong> <br>\r
- <em>Functions for calculating trees on the alignment or the currently\r
+ <em>Functions for calculating trees on the alignment or the currently \r
selected region. See <a\r
- href="../calculations/tree.html">calculating trees</a>.</em>\r
+ href="../calculations/tree.html">calculating trees</a>.</em> \r
<ul>\r
<li><strong>Average Distance Using % Identity</strong></li>\r
<li><strong>Neighbour Joining Using % Identity</strong></li>\r
</ul>\r
</li>\r
<li><strong>Pairwise Alignments</strong><br>\r
- <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise\r
+ <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise \r
alignments</a>.</em></li>\r
<li><strong>Principal Component Analysis</strong><br>\r
- <em>Shows a spatial clustering of the sequences based on the BLOSUM62\r
- scores in the alignment. See <a href="../calculations/pca.html">Principal\r
+ <em>Shows a spatial clustering of the sequences based on the BLOSUM62 \r
+ scores in the alignment. See <a href="../calculations/pca.html">Principal \r
Component Analysis</a>.</em> </li>\r
<li><strong>Translate cDNA</strong><br>\r
- <em>If you are viewing a cDNA alignment a very simple translation service\r
- is available. The translation ignores all gaps in the cDNA sequences.\r
+ <em>If you are viewing a cDNA alignment a very simple translation service \r
+ is available. The translation ignores all gaps in the cDNA sequences. \r
</em> <br>\r
</li>\r
</ul>\r
</li>\r
<li><strong>Web Service<br>\r
- </strong> <em>Selecting one of the following menu items starts a remote service\r
- on compute facilities at the University of Dundee. You need a continuous network\r
- connection in order to use these services through Jalview. </em>\r
+ </strong> <em>Selecting one of the following menu items starts a remote service \r
+ on compute facilities at the University of Dundee. You need a continuous network \r
+ connection in order to use these services through Jalview. </em> \r
<ul>\r
- <li><strong>Alignment </strong>\r
+ <li><strong>Alignment </strong> \r
<ul>\r
<li><strong>ClustalW Multiple Sequence Alignment</strong><br>\r
- <em> Submits all, or just the currently selected sequences for alignment\r
+ <em> Submits all, or just the currently selected sequences for alignment \r
with clustal W.</em></li>\r
<li><strong>ClustalW Multiple Sequence Alignment Realign</strong><br>\r
- <em> Submits the alignment or currently selected region for re-alignment\r
- with clustal W. Use this if you have added some new sequences to an\r
+ <em> Submits the alignment or currently selected region for re-alignment \r
+ with clustal W. Use this if you have added some new sequences to an \r
existing alignment.</em></li>\r
<li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>\r
- <em> Submits all, or jut the currently selected sequences for alignment\r
- using Muscle. Do not use this if you are working with nucleic acid\r
+ <em> Submits all, or jut the currently selected sequences for alignment \r
+ using Muscle. Do not use this if you are working with nucleic acid \r
sequences.</em></li>\r
</ul>\r
</li>\r
- <li><strong>Secondary Structure Prediction</strong>\r
+ <li><strong>Secondary Structure Prediction</strong> \r
<ul>\r
<li><strong>JPred Secondary Structure Prediction</strong><br>\r
- <em>Secondary structure prediction by network consensus. The behaviour\r
+ <em>Secondary structure prediction by network consensus. The behaviour \r
of this calculation depends on the current selection: </em></li>\r
- <li><em>If nothing is selected, and the displayed sequences appear to\r
- be aligned, then a JNet prediction will be run for the first sequence\r
- in the alignment, using the current alignment. Otherwise the first\r
+ <li><em>If nothing is selected, and the displayed sequences appear to \r
+ be aligned, then a JNet prediction will be run for the first sequence \r
+ in the alignment, using the current alignment. Otherwise the first \r
sequence will be submitted for prediction. </em></li>\r
- <li><em>If just one sequence (or a region on one sequence) has been\r
- selected, it will be submitted to the automatic JNet prediction server\r
+ <li><em>If just one sequence (or a region on one sequence) has been \r
+ selected, it will be submitted to the automatic JNet prediction server \r
for homolog detection and prediction. </em></li>\r
- <li><em>If a set of sequences are selected, and they appear to be aligned,\r
- then the alignment will be used for a Jnet prediction on the <strong>first</strong>\r
- sequence selected in the set (that is, the one that was first clicked\r
+ <li><em>If a set of sequences are selected, and they appear to be aligned, \r
+ then the alignment will be used for a Jnet prediction on the <strong>first</strong> \r
+ sequence selected in the set (that is, the one that was first clicked \r
on). </em> </li>\r
</ul>\r
</li>\r
git://source.jalview.org / jalview.git / commitdiff