2 <head><title>Alignment Window Menus</title></head>
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5 <p><strong>Alignment Window Menus</strong></p>
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7 <li><strong>File</strong>
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9 <li><strong>Save As<br>
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10 </strong><em>Save the alignment to local file. A file selection window
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11 will open, use the "Files of type:" selection box to determine
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12 which <a href="../io/index.html">alignment format</a> to save as.</em></li>
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13 <li><strong>Export</strong> <em><br>
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14 Creates an alignment graphic with the current annotation, alignment background
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15 colours and group colours. If the alignment is <a
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16 href="../features/wrap.html">wrapped</a>, the output will also be wrapped
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17 and will have the same visible residue width as the open alignment. </em>
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19 <li><strong>HTML<br>
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20 </strong><em>Create a <a href="../io/index.html#export">web page</a>
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21 from your alignment.</em></li>
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23 </strong><em>Create an <a href="../io/index.html#export">Encapsulated
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24 Postscript</a> file from your alignment.</em></li>
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26 </strong><em>Create a <a href="../io/index.html#export">Portable Network
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27 Graphics</a> file from your alignment.</em></li>
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30 <li><strong>Output to Textbox<br>
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31 </strong><em>The alignment will be displayed in plain text in a new window
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32 which you can "Copy and Paste" using the pull down menu, or
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33 your standard operating system copy and paste keys. <br>
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34 Select the format of the text by selecting one of the following menu items.</em>
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36 <li><strong>FASTA</strong> <em></em></li>
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37 <li><strong>MSF</strong></li>
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38 <li><strong>CLUSTAL</strong></li>
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39 <li><strong>BLC</strong></li>
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40 <li><strong>PIR</strong></li>
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41 <li><strong>PFAM</strong></li>
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44 <li><strong>Print<br>
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45 </strong><em>Jalview will print the alignment using the current fonts
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46 and colours of your alignment. If the alignment has annotations visible,
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47 these will be printed below the alignment. If the alignment is wrapped
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48 the number of residues per line of your alignment will depend on the paper
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49 width or your alignment window width, whichever is the smaller. </em></li>
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50 <li><strong>Load Associated Tree<br>
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51 </strong><em>Jalview can <a
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52 href="../calculations/treeviewer.html">view trees</a> stored in the Newick
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53 file format, and associate them with the alignment. Note: the ids of the
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54 tree file and your alignment MUST be the same.</em></li>
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55 <li><strong>Close<br>
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56 </strong><em>Close the alignment window. Make sure you have saved your
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57 alignment before you close - either as a Jalview project or by using the
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58 <strong>Save As</strong> menu.<br>
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62 <li><strong>Edit</strong>
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64 <li><strong>Undo</strong><em><br>
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65 This will undo any edits you make to the alignment. This applies to insertion
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66 or deletion of gaps, cutting residues or sequences from the alignment
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67 or pasting sequences to the current alignment or sorting the alignment.
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68 <strong>NOTE:</strong> It DOES NOT undo colour changes, adjustments to
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69 group sizes, or changes to the annotation panel. </em></li>
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70 <li><strong>Redo<br>
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71 </strong><em>Any actions which you undo can be redone using redo. </em></li>
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73 </strong><em>This will make a copy of the currently selected residues
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74 before removing them from your alignment. Click on a sequence name if
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75 you wish to select a whole sequence. <br>
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76 Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>
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77 <li><strong>Copy</strong><br>
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78 <em>Copies the currently selected residues to the system clipboard - you
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79 can also do this by pressing <CTRL> and C (<APPLE> and C on
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81 If you try to paste the clipboard contents to a text editor, you will
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82 see the format of the copied residues FASTA.</em></li>
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83 <li><strong>Paste </strong>
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85 <li><strong>To New Alignment<br>
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86 </strong><em>A new alignment window will be created from sequences
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87 previously copied or cut to the system clipboard. <br>
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88 Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.</em></li>
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89 <li><strong>Add To This Alignment<br>
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90 </strong><em>Copied sequences from another alignment window can be
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91 added to the current Jalview alignment. </em></li>
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94 <li><strong>Delete<br>
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95 </strong><em>This will delete the currently selected residues without
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96 copying them to the clipboard. Like the other edit operations, this can
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97 be undone with <strong>Undo</strong>.</em></li>
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98 <li><strong>Select All<br>
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99 </strong><em>Selects all the sequences and residues in the alignment.
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101 Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.</em></li>
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102 <li><strong>Deselect All<br>
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103 </strong><em>Removes the current selection box (red dashed box) from the
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104 alignment window. All selected sequences, residues and marked columns
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105 will be deselected. </em><em> <br>
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106 Use <ESCAPE> to deselect all.</em></li>
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107 <li><strong>Invert Selection<br>
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108 </strong><em>Any sequence ids currently not selected will replace the
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109 current selection. </em></li>
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110 <li><strong>Undefine Groups<br>
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111 </strong><em>The alignment will be reset with no defined groups.<br>
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112 <strong>WARNING</strong>: This cannot be undone.</em></li>
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113 <li><strong>Remove Left<br>
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114 </strong><em>If the alignment has marked columns, the alignment will be
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115 trimmed to the left of the leftmost marked column. To mark a column, mouse
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116 click the scale bar above the alignment. Click again to unmark a column,
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117 or select "Deselect All" to deselect all columns.</em></li>
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118 <li><strong>Remove Right<br>
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119 </strong><em>If the alignment has marked columns, the alignment will be
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120 trimmed to the left of the leftmost marked column. To mark a column, mouse
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121 click the scale bar above the alignment. Click again to unmark a column,
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122 or select "Deselect All" to deselect all columns.</em></li>
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123 <li><strong>Remove Empty Columns<br>
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124 </strong><em>All columns which only contain gap characters ("-",
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125 ".") will be deleted.<br>
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126 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
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128 <li><strong>Remove All Gaps</strong><br>
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129 <em>Gap characters ("-", ".") will be deleted from
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130 the selected area of the alignment. If no selection is made, ALL the gaps
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131 in the alignment will be removed.<br>
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132 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
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134 <li><strong>Remove Redundancy<br>
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135 </strong><em>Selecting this option brings up a window asking you to select
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136 a threshold. If the percentage identity between any two sequences (under
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137 the current alignment) exceeds this value then one of the sequences (the
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138 shorter) is discarded. Press the "Apply" button to remove redundant
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139 sequences. The "Undo" button will undo the last redundancy deletion.</em></li>
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140 <li><strong>Pad Gaps<br>
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141 </strong><em>Adds gaps to the end of all the sequences so they are all
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142 the same length. This is useful for making a tree using unaligned sequences.<br>
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143 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
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148 <li><strong>Search</strong>
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150 <li><strong>Find<br>
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151 </strong><em>Select this to <a href="../features/search.html">search</a>
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152 for residues, sequence name or residue position within the alignment.
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157 <li><strong>View</strong>
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159 <li><strong>Font<br>
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160 </strong><em>Change the font of the display from the "Choose Font"
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161 dialog box, which is shown when this item is selected. </em></li>
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162 <li><strong>Wrap<br>
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163 </strong><em>When ticked, the alignment display is "<a href="../features/wrap.html">wrapped</a>"
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164 to the width of the alignment window. This is useful if your alignment
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165 has only a few sequences to view its full width at once.<br>
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166 Options are available to show the residue numbering at the start and/or
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167 end of an alignment as well as showing the alignment position above each
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169 <strong>NOTE</strong>: When in wrapped alignment view, the alignment cannot
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170 be edited or have regions selected on it. </em></li>
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171 <li><strong>Show Full Sequence ID<br>
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172 </strong><em>If this box is selected the sequence name will have the start
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173 and end position of the sequence appended to the name, in the format NAME/START-END</em></li>
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174 <li><strong>Boxes</strong><em><br>
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175 If this is selected the background of a residue will be coloured using
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176 the selected background colour. Useful if used in conjunction with "Colour
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177 Text." </em></li>
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178 <li><strong>Text<br>
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179 </strong><em>If this is selected the residues will be displayed using
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180 the standard 1 character amino acid alphabet.</em></li>
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181 <li><strong>Colour Text<br>
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182 </strong><em>If this is selected the residues will be coloured according
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183 to the background colour associated with that residue. The colour is slightly
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184 darker than background so the amino acid symbol remains visible. </em></li>
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185 <li><strong>Show Gaps<br>
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186 </strong><em>When this is selected, gap characters will be displayed as
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187 "." or "-". If unselected, then gap characters will
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188 appear as blank spaces. <br>
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189 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.</em></li>
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190 <li><strong>Show Annotations<br>
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191 </strong><em>If this is selected the "Annotation Panel" will
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192 be displayed below the alignment. The default setting is to display the
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193 conservation calculation, quality calculation and consensus values as
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194 bar charts. </em></li>
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195 <li><strong>Sequence Features<br>
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196 </strong><em>If the sequence names are Swissprot entries Jalview will
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197 use the names to retrieve <a href="../features/seqfeatures.html">sequence
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198 features</a> from the EBI. Features which are 1 residue in length are
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199 coloured red, sequences longer than 1 residue are coloured blue. Move
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200 the mouse over a coloured feature to display the details of the feature.
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202 Note: The retrieved information will update the sequence start and end
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203 labels if they are incorrect. </em></li>
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204 <li><strong><a href="../features/overview.html">Overview Window</a><br>
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205 </strong><em>A scaled version of the alignment will be displayed in a
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206 small window. A red box will indicate the currently visible area of the
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207 alignment. Move the visible region using the mouse. </em><strong> </strong></li>
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210 <li><strong>Colour</strong>
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212 <li><strong>Apply Colour To All Groups<br>
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213 </strong><em>If this is selected, any changes made to the background colour
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214 will be applied to all currently defined groups.</em></li>
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215 <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage
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216 Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,
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217 Turn Propensity, Buried Index, Nucleotide, User Defined<br>
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218 </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
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219 a description of all colour schemes.</em></li>
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220 <li><strong>By Conservation<br>
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221 </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
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222 by Conservation</a>.</em></li>
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223 <li><strong>Modify Conservation Threshold<br>
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224 </strong><em>Use this to display the conservation threshold slider window.
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225 Useful if the window has been closed, or if the 'by conservation' option
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226 appears to be doing nothing!</em></li>
\r
227 <li><strong>Above Identity Threshold<br>
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228 </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage
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229 Identity</a></em><strong>.</strong></li>
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230 <li><strong>Modify Identity Threshold<br>
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231 </strong><em>Use this to set the threshold value for colouring above Identity.
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232 Useful if the window has been closed. <br>
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236 <li><strong>Calculate</strong>
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240 <li><strong>by ID</strong><em><br>
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241 This will sort the sequences according to sequence name. If the sort
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242 is repeated, the order of the sorted sequences will be inverted. </em></li>
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243 <li><strong>by Group</strong><strong><br>
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244 </strong><em>This will sort the sequences according to sequence name.
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245 If the sort is repeated, the order of the sorted sequences will be
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246 inverted. </em><strong></strong></li>
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247 <li><strong>by Pairwise Identity<br>
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248 </strong><em>This will sort the selected sequences by their percentage
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249 identity to the consensus sequence. The most similar sequence is put
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250 at the top. </em></li>
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251 <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will
\r
252 have some additional options if you have just done a multiple alignment
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253 calculation, or opened a tree viewer window.</em></li>
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256 <li><strong>Calculate Tree </strong> <br>
\r
257 <em>Functions for calculating trees on the alignment or the currently
\r
258 selected region. See <a
\r
259 href="../calculations/tree.html">calculating trees</a>.</em>
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261 <li><strong>Average Distance Using % Identity</strong></li>
\r
262 <li><strong>Neighbour Joining Using % Identity</strong></li>
\r
263 <li><strong>Average Distance Using Blosum62</strong></li>
\r
264 <li><strong>Neighbour Joining Using Blosum62</strong></li>
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267 <li><strong>Pairwise Alignments</strong><br>
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268 <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise
\r
269 alignments</a>.</em></li>
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270 <li><strong>Principal Component Analysis</strong><br>
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271 <em>Shows a spatial clustering of the sequences based on the BLOSUM62
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272 scores in the alignment. See <a href="../calculations/pca.html">Principal
\r
273 Component Analysis</a>.</em> <br>
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277 <li><strong>Web Service<br>
\r
278 </strong> <em>Selecting one of the following menu items starts a remote service
\r
279 on compute facilities at the University of Dundee. You need a continuous network
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280 connection in order to use these services through Jalview. </em>
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282 <li><strong>Alignment </strong>
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284 <li><strong>ClustalW Multiple Sequence Alignment</strong><br>
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285 <em> Submits all, or just the currently selected sequences for alignment
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286 with clustal W.</em></li>
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287 <li><strong>ClustalW Multiple Sequence Alignment Realign</strong><br>
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288 <em> Submits the alignment or currently selected region for re-alignment
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289 with clustal W. Use this if you have added some new sequences to an
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290 existing alignment.</em></li>
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291 <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>
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292 <em> Submits all, or jut the currently selected sequences for alignment
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293 using Muscle. Do not use this if you are working with nucleic acid
\r
294 sequences.</em></li>
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297 <li><strong>Secondary Structure Prediction</strong>
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299 <li><strong>JPred Secondary Structure Prediction</strong><br>
\r
300 <em>Secondary structure prediction by network consensus. The behaviour
\r
301 of this calculation depends on the current selection: </em></li>
\r
302 <li><em>If nothing is selected, and the displayed sequences appear to
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303 be aligned, then a JNet prediction will be run for the first sequence
\r
304 in the alignment, using the current alignment. Otherwise the first
\r
305 sequence will be submitted for prediction. </em></li>
\r
306 <li><em>If just one sequence (or a region on one sequence) has been
\r
307 selected, it will be submitted to the automatic JNet prediction server
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308 for homolog detection and prediction. </em></li>
\r
309 <li><em>If a set of sequences are selected, and they appear to be aligned,
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310 then the alignment will be used for a Jnet prediction on the <strong>first</strong>
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311 sequence selected in the set (that is, the one that was first clicked
\r