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></li>
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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 will
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11 open, use the "Files of type:" selection box to determine which
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12 <a href="../io/index.html">alignment format</a> to save as.<br>
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14 <li><strong>Export</strong> <em><br>
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15 Creates an alignment graphic with the current annotation,
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16 alignment background colours and group colours. If the alignment is <a
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17 href="../features/wrap.html">wrapped</a>, the output will also
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18 be wrapped and will have the same visible residue width as the
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22 <li><strong>HTML<br>
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23 </strong><em>Create a <a href="../io/index.html#export">web page</a>
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24 from your alignment.</em></li>
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26 </strong><em>Create an <a href="../io/index.html#export">Encapsulated
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27 Postscript</a> file from your alignment.</em></li>
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29 </strong><em>Create a <a href="../io/index.html#export">Portable Network
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30 Graphics</a> file from your alignment.<br>
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34 <li><strong>Output to Textbox<br>
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35 </strong><em>The alignment will be displayed in plain text in a new window
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36 which you can "Copy and Paste" using the pull down menu, or your
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37 standard operating system copy and paste keys. <br>
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38 Select the format of the text by selecting one of the following menu items.</em>
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40 <li><strong>FASTA</strong> <em></em></li>
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41 <li><strong>MSF</strong></li>
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42 <li><strong>CLUSTAL</strong></li>
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43 <li><strong>BLC</strong></li>
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44 <li><strong>PIR</strong></li>
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45 <li><strong>PFAM</strong><br></li>
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48 <li><strong>Print<br>
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49 </strong><em>Jalview will print the alignment using the current fonts and
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50 colours of your alignment. If the alignment has annotations visible, these
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51 will be printed below the alignment. If the alignment is wrapped the number
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52 of residues per line of your alignment will depend on the paper width or
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53 your alignment window width, whichever is the smaller. <br>
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55 <li><strong>Load Associated Tree<br>
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56 </strong><em>Jalview can <a
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57 href="../calculations/treeviewer.html">view trees</a> stored in
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58 the Newick file format, and associate them with the
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59 alignment. Note: the ids of the tree file and your alignment
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60 MUST be the same.<br>
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62 <li><strong>Close<br>
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63 </strong><em>Close the alignment window. Make sure you have
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64 saved your alignment before you close - either as a Jalview
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65 project or by using the <strong>Save As</strong> menu.<br>
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68 <li><strong>Edit</strong></li>
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72 <li><strong>Undo</strong><em><br>
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73 This will undo any edits you make to the alignment. This applies to insertion
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74 or deletion of gaps, cutting residues or sequences from the alignment or
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75 pasting sequences to the current alignment or sorting the
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76 alignment. <strong>NOTE:</strong> It DOES NOT undo colour
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77 changes, adjustments to group sizes, or changes to the annotation panel. <br>
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79 <li><strong>Redo<br>
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80 </strong><em>Any actions which you undo can be redone using redo. <br>
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83 </strong><em>This will make a copy of the currently selected residues before
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84 removing them from your alignment. Click on a sequence name if you wish
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85 to select a whole sequence. <br>
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86 Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.<br>
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88 <li><strong>Copy</strong><br>
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89 <em>Copies the currently selected residues to the system
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90 clipboard - you can also do this by pressing <CTRL> and C
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91 (<APPLE> and C on MacOSX). <br>
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92 If you try to paste the clipboard contents to a text editor, you will see
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93 the format of the copied residues is a tab separated list:<br>
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95 NAME START_RES END_RES SEQUENCE
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98 <li><strong>Paste </strong>
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100 <li><strong>To New Alignment<br>
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101 </strong><em>A new alignment window will be created from sequences previously
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102 copied or cut to the system clipboard. <br>
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103 Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.</em></li>
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104 <li><strong>Add To This Alignment<br>
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105 </strong><em>Copied sequences from another alignment window can be added
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106 to the current Jalview alignment. <br>
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107 </em><strong> </strong></li>
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110 <li><strong>Delete<br>
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111 </strong><em>This will delete the currently selected residues
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112 without copying them to the clipboard. Like the other edit
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113 operations, this can be undone with <strong>Undo</strong>.<br>
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115 <li><strong>Select All<br>
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116 </strong><em>Selects all the sequences and residues in the alignment. <br>
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117 Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.<br>
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119 <li><strong>Deselect All<br>
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120 </strong><em>Removes the current selection box (red dashed box) from the
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121 alignment window. All selected sequences, residues and marked columns will
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122 be deselected. </em><em> <br>
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123 Use <ESCAPE> to deselect all.<br>
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125 <li><strong>Invert Selection<br>
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126 </strong><em>Any sequence ids currently not selected will replace the current
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128 </em><strong> </strong></li>
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129 <li><strong>Undefine Groups<br>
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130 </strong><em>The alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:
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131 This cannot be undone.<br>
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133 <li><strong>Remove Left<br>
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134 </strong><em>If the alignment has marked columns, the alignment will be
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135 trimmed to the left of the leftmost marked column. To mark a column, mouse
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136 click the scale bar above the alignment. Click again to unmark a column,
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137 or select "Deselect All" to deselect all columns.<br>
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139 <li><strong>Remove Right<br>
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140 </strong><em>If the alignment has marked columns, the alignment will be
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141 trimmed to the left of the leftmost marked column. To mark a column, mouse
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142 click the scale bar above the alignment. Click again to unmark a column,
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143 or select "Deselect All" to deselect all columns.<br>
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145 <li><strong>Remove Empty Columns<br>
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146 </strong><em>All columns which only contain gap characters ("-",
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147 ".") will be deleted.<br>
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148 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
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151 <li><strong>Remove All Gaps</strong><br>
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152 <em><strong>All</strong> gap characters ("-", ".") will be deleted from
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154 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
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157 <li><strong>Remove Redundancy<br>
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158 </strong><em>Selecting this option brings up a window asking you to select
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159 a threshold. If the percentage identity between any two sequences
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160 (under the current alignment) exceeds this
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161 value then one of the sequences (the shorter) is discarded. Press the "Apply"
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162 button to remove redundant sequences. The "Undo" button will undo the last
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163 redundancy deletion.<br>
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165 <li><strong>Pad Gaps<br>
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166 </strong><em>Adds gaps to the end of all the sequences so they
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167 are all the same length. This is useful for making a tree using
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168 unaligned sequences.<br>
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169 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
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174 <li><strong>Search</strong></li>
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178 <li><strong>Find<br>
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179 </strong><em>Select this to <a href="../features/search.html">search</a>
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180 for residues, sequence name or residue position within the alignment. </em></li>
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184 <li><strong>View</strong></li>
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188 <li><strong>Font<br>
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189 </strong><em>Change the font of the display from the
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190 "Choose Font" dialog box, which is shown when this
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191 item is selected. <br>
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193 <li><strong>Wrap<br>
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194 </strong><em>When ticked, the alignment display is
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195 "<a href="../features/wrap.html">wrapped</a>" to the
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196 width of the alignment window. This is useful if your alignment
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197 has only a few sequences to view its full width at once.<br>
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198 Options are available to show the residue numbering at the start and/or
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199 end of an alignment as well as showing the alignment position above each
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201 <strong>NOTE</strong>: When in wrapped alignment view, the
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202 alignment cannot be edited or have regions selected on it. <br>
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203 </em><strong> </strong></li>
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204 <li><strong>Show Full Sequence ID<br>
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205 </strong><em>If this box is selected the sequence name will have the start
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206 and end position of the sequence appended to the name, in the format NAME/START-END<br>
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208 <li><strong>Boxes</strong><em><br>
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209 If this is selected the background of a residue will be coloured using the
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210 selected background colour. Useful if used in conjunction with "Colour
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213 <li><strong>Text<br>
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214 </strong><em>If this is selected the residues will be displayed using the
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215 standard 1 character amino acid alphabet.<br>
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217 <li><strong>Colour Text<br>
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218 </strong><em>If this is selected the residues will be coloured according
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219 to the background colour associated with that residue. The colour is slightly
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220 darker than background so the amino acid symbol remains visible. <br>
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222 <li><strong>Show Gaps<br>
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223 </strong><em>When this is selected, gap characters will be displayed as "."
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224 or "-". If unselected, then gap characters will appear as blank spaces.
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226 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.<br>
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228 <li><strong>Show Annotations<br>
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229 </strong><em>If this is selected the "Annotation Panel" will be
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230 displayed below the alignment. The default setting is to display the conservation
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231 calculation, quality calculation and consensus values as bar charts. </em><br>
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233 <li><strong>Sequence Features<br>
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234 </strong><em>If the sequence names are Swissprot entries Jalview will use
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235 the names to retrieve <a href="../features/seqfeatures.html">sequence features</a> from the EBI. Features which are
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236 1 residue in length are coloured red, sequences longer than 1 residue are
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237 coloured blue. Move the mouse over a coloured feature to display the details
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238 of the feature. <br>
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239 Note: The retrieved information will update the sequence start and end labels
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240 if they are incorrect. <br>
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242 <li><strong><a href="../features/overview.html">Overview Window</a><br>
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243 </strong><em>A scaled version of the alignment will be displayed in a small
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244 window. A red box will indicate the currently visible area of the alignment.
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245 Move the visible region using the mouse. </em><strong> </strong></li>
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249 <li><strong>Colour</strong></li>
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253 <li><strong>Apply Colour To All Groups<br>
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254 </strong><em>If this is selected, any changes made to the background colour
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255 will be applied to all currently defined groups.<br>
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257 <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor,
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258 Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried
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259 Index, Nucleotide, User Defined<br>
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260 </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
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261 a description of all colour schemes.</em><br>
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263 <li><strong>By Conservation<br>
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264 </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
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265 by Conservation</a>.</em><br>
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267 <li><strong>Modify Conservation Threshold<br>
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268 </strong><em>Use this to display the conservation threshold slider window.
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269 Useful if the window has been closed, or if the 'by
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270 conservation' option appears to be doing nothing!</em><br></li>
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271 <li><strong>Above Identity Threshold<br>
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272 </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage
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273 Identity</a></em><strong>.<br>
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275 <li><strong>Modify Identity Threshold<br>
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276 </strong><em>Use this to set the threshold value for colouring above Identity.
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277 Useful if the window has been closed. </em></li>
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281 <li><strong>Calculate</strong></li>
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285 <li><strong>Sort </strong>
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287 <li><strong>by ID<br>
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288 </strong><em>This will sort the sequences according to sequence name.
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289 If the sort is repeated, the order of the sorted sequences will be inverted.
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292 <li><strong>by Group</strong><strong><br>
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293 </strong><em>This will sort the sequences according to sequence name.
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294 If the sort is repeated, the order of the sorted sequences will be inverted.
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295 </em><strong></strong><strong><br>
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297 <li><strong>by Pairwise Identity<br>
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298 </strong><em>This will sort the selected sequences by their percentage
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299 identity to the consensus sequence. The most similar sequence is put
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300 at the top. </em><strong><br>
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303 <em>The <a href="../calculations/sorting.html">Sort menu</a> will
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304 have some additional options if you have just done a multiple
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305 alignment calculation, or opened a tree viewer window.</em><br>
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307 <li><strong>Calculate Tree </strong>
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308 <br><em>Functions for calculating trees on the alignment or the
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309 currently selected region. See <a
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310 href="../calculations/tree.html">calculating trees</a>.</em>
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312 <li><strong>Average Distance Using % Identity</strong></li>
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313 <li><strong>Neighbour Joining Using % Identity</strong></li>
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314 <li><strong>Average Distance Using Blosum62</strong></li>
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315 <li><strong>Neighbour Joining Using Blosum62<br></strong></li>
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318 <li><strong>Pairwise Alignments</strong><br>
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319 <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
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321 <li><strong>Principal Component Analysis</strong><br>
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322 <em>Shows a spatial clustering of the sequences based on the
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323 BLOSUM62 scores in the alignment. See <a href="../calculations/pca.html">Principal Component Analysis</a>.</em>
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326 <li><strong>Web Service<br>
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328 <em>Selecting one of the following menu items starts a remote service
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329 on compute facilities at the University of Dundee. You need a
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330 continuous network connection in order to use these services
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334 <li><strong>Clustal Alignment</strong><br><em>
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335 Submits all, or just the currently selected sequences for alignment with clustal W.</em><br></li>
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336 <li><strong>Clustal Realign</strong><br><em>
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337 Submits the alignment or currently selected region for
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338 re-alignment with clustal W. Use this if you have added some
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339 new sequences to an existing alignment.</em><br></li>
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340 <li><strong>Muscle Alignment</strong><br><em>
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341 Submits all, or jut the currently selected sequences for
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342 alignment using Muscle. Do not use this if you are working with
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343 nucleic acid sequences.</em><br>
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344 <li><strong>JNet</strong><br><em>
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345 Secondary structure prediction by network consensus. The
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346 behaviour of this calculation depends on the current selection:
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348 <li>If nothing is selected, and the displayed sequences appear to
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349 be aligned, then a JNet prediction will be run for the first
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350 sequence in the alignment, using the current
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351 alignment. Otherwise the first sequence will be submitted for prediction.
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354 just one sequence (or a region on one sequence) has been selected,
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355 it will be submitted to the automatic JNet prediction server
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356 for homolog detection and prediction.
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358 <li>If a set of sequences are selected, and they appear to be aligned,
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359 then the alignment will be used for a Jnet prediction on the
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360 <strong>first</strong> sequence selected in the set (that is, the one
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361 that was first clicked on).
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git://source.jalview.org / jalview.git / blob