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>Fetch Sequence</strong><br>
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10 <em>Shows a dialog window in which you can select known ids from Uniprot,
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11 EMBL, EMBLCDS or PDB database using Web Services provided by the European
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12 Bioinformatics Institute. See <a href="../features/seqfetch.html">Sequence
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13 Fetcher</a></em>.</li>
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14 <li><strong>Save As<br>
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15 </strong><em>Save the alignment to local file. A file selection window
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16 will open, use the "Files of type:" selection box to determine
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17 which <a href="../io/index.html">alignment format</a> to save as.</em></li>
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18 <li><strong>Export</strong> <em><br>
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19 Creates an alignment graphic with the current annotation, alignment background
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20 colours and group colours. If the alignment is <a
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21 href="../features/wrap.html">wrapped</a>, the output will also be wrapped
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22 and will have the same visible residue width as the open alignment. </em>
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24 <li><strong>HTML<br>
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25 </strong><em>Create a <a href="../io/index.html#export">web page</a>
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26 from your alignment.</em></li>
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28 </strong><em>Create an <a href="../io/index.html#export">Encapsulated
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29 Postscript</a> file from your alignment.</em></li>
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31 </strong><em>Create a <a href="../io/index.html#export">Portable Network
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32 Graphics</a> file from your alignment.</em></li>
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35 <li><strong>Output to Textbox<br>
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36 </strong><em>The alignment will be displayed in plain text in a new window
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37 which you can "Copy and Paste" using the pull down menu, or
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38 your standard operating system copy and paste keys. <br>
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39 Select the format of the text by selecting one of the following menu items.</em>
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41 <li><strong>FASTA</strong> <em></em></li>
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42 <li><strong>MSF</strong></li>
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43 <li><strong>CLUSTAL</strong></li>
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44 <li><strong>BLC</strong></li>
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45 <li><strong>PIR</strong></li>
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46 <li><strong>PFAM</strong></li>
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49 <li><strong>Print<br>
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50 </strong><em>Jalview will print the alignment using the current fonts
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51 and colours of your alignment. If the alignment has annotations visible,
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52 these will be printed below the alignment. If the alignment is wrapped
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53 the number of residues per line of your alignment will depend on the paper
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54 width or your alignment window width, whichever is the smaller. </em></li>
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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 the Newick
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58 file format, and associate them with the alignment. Note: the ids of the
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59 tree file and your alignment MUST be the same.</em></li>
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60 <li><strong>Load Features / Annotations<br>
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61 </strong><em>Jalview load precalculated <a href="../features/featuresFormat.html">sequence
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62 features</a> or <a href="../features/annotationsFormat.html">alignment
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63 annotations</a>.</em></li>
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64 <li><strong>Close<br>
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65 </strong><em>Close the alignment window. Make sure you have saved your
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66 alignment before you close - either as a Jalview project or by using the
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67 <strong>Save As</strong> menu.<br>
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71 <li><strong>Edit</strong>
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73 <li><strong>Undo</strong><em><br>
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74 This will undo any edits you make to the alignment. This applies to insertion
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75 or deletion of gaps, cutting residues or sequences from the alignment
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76 or pasting sequences to the current alignment or sorting the alignment.
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77 <strong>NOTE:</strong> It DOES NOT undo colour changes, adjustments to
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78 group sizes, or changes to the annotation panel. </em></li>
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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. </em></li>
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82 </strong><em>This will make a copy of the currently selected residues
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83 before removing them from your alignment. Click on a sequence name if
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84 you wish to select a whole sequence. <br>
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85 Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>
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86 <li><strong>Copy</strong><br>
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87 <em>Copies the currently selected residues to the system clipboard - you
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88 can also do this by pressing <CTRL> and C (<APPLE> and C on
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90 If you try to paste the clipboard contents to a text editor, you will
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91 see the format of the copied residues FASTA.</em></li>
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92 <li><strong>Paste </strong>
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94 <li><strong>To New Alignment<br>
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95 </strong><em>A new alignment window will be created from sequences
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96 previously copied or cut to the system clipboard. <br>
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97 Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.</em></li>
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98 <li><strong>Add To This Alignment<br>
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99 </strong><em>Copied sequences from another alignment window can be
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100 added to the current Jalview alignment. </em></li>
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103 <li><strong>Delete<br>
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104 </strong><em>This will delete the currently selected residues without
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105 copying them to the clipboard. Like the other edit operations, this can
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106 be undone with <strong>Undo</strong>.</em></li>
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107 <li><strong>Select All<br>
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108 </strong><em>Selects all the sequences and residues in the alignment.
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110 Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.</em></li>
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111 <li><strong>Deselect All<br>
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112 </strong><em>Removes the current selection box (red dashed box) from the
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113 alignment window. All selected sequences, residues and marked columns
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114 will be deselected. </em><em> <br>
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115 Use <ESCAPE> to deselect all.</em></li>
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116 <li><strong>Invert Selection<br>
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117 </strong><em>Any sequence ids currently not selected will replace the
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118 current selection. </em></li>
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119 <li><strong>Undefine Groups<br>
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120 </strong><em>The alignment will be reset with no defined groups.<br>
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121 <strong>WARNING</strong>: This cannot be undone.</em></li>
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122 <li><strong>Remove Left<br>
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123 </strong><em>If the alignment has marked columns, the alignment will be
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124 trimmed to the left of the leftmost marked column. To mark a column, mouse
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125 click the scale bar above the alignment. Click again to unmark a column,
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126 or select "Deselect All" to deselect all columns.</em></li>
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127 <li><strong>Remove Right<br>
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128 </strong><em>If the alignment has marked columns, the alignment will be
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129 trimmed to the left of the leftmost marked column. To mark a column, mouse
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130 click the scale bar above the alignment. Click again to unmark a column,
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131 or select "Deselect All" to deselect all columns.</em></li>
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132 <li><strong>Remove Empty Columns<br>
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133 </strong><em>All columns which only contain gap characters ("-",
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134 ".") will be deleted.<br>
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135 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
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137 <li><strong>Remove All Gaps</strong><br>
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138 <em>Gap characters ("-", ".") will be deleted from
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139 the selected area of the alignment. If no selection is made, ALL the gaps
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140 in the alignment will be removed.<br>
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141 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
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143 <li><strong>Remove Redundancy<br>
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144 </strong><em>Selecting this option brings up a window asking you to select
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145 a threshold. If the percentage identity between any two sequences (under
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146 the current alignment) exceeds this value then one of the sequences (the
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147 shorter) is discarded. Press the "Apply" button to remove redundant
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148 sequences. The "Undo" button will undo the last redundancy deletion.</em></li>
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149 <li><strong>Pad Gaps<br>
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150 </strong><em>When selected, the alignment will be kept at minimal
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151 width (so there no empty columns before or after the first or last aligned
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152 residue) and all sequences will be padded with gap characters to
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153 the before and after their terminating residues.<br>
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154 This switch is useful when making a tree using unaligned
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155 sequences and when working with alignment analysis programs which
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156 require 'properly aligned sequences' to be all the same length.<br>
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157 You may set the default for <strong>Pad Gaps</strong> in the <a href="../features/preferences.html">preferences</a>.
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163 <li><strong>Search</strong>
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165 <li><strong>Find<br>
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166 </strong><em>Select this to <a href="../features/search.html">search</a>
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167 for residues, sequence name or residue position within the
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168 alignment and create new sequence features from the queries.
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173 <li><strong>View</strong>
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175 <li><strong>Font<br>
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176 </strong><em>Change the font of the display from the "Choose Font"
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177 dialog box, which is shown when this item is selected. </em></li>
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178 <li><strong>Smooth Fonts</strong><em><br>
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179 If selected, the alignment will be drawn with anti-aliasing on which looks
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180 better, but performace is reduced.
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182 <li><strong>Wrap<br>
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183 </strong><em>When ticked, the alignment display is "<a href="../features/wrap.html">wrapped</a>"
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184 to the width of the alignment window. This is useful if your alignment
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185 has only a few sequences to view its full width at once.<br>
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186 Options are available to show the residue numbering at the start and/or
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187 end of an alignment as well as showing the alignment position above each
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189 <strong>NOTE</strong>: When in wrapped alignment view, the alignment cannot
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190 be edited or have regions selected on it. </em></li>
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191 <li><strong>Show Full Sequence ID<br>
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192 </strong><em>If this box is selected the sequence name will have the start
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193 and end position of the sequence appended to the name, in the format NAME/START-END</em></li>
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194 <li><strong>Boxes</strong><em><br>
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195 If this is selected the background of a residue will be coloured using
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196 the selected background colour. Useful if used in conjunction with "Colour
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197 Text." </em></li>
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198 <li><strong>Text<br>
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199 </strong><em>If this is selected the residues will be displayed using
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200 the standard 1 character amino acid alphabet.</em></li>
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201 <li><strong>Colour Text<br>
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202 </strong><em>If this is selected the residues will be coloured according
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203 to the background colour associated with that residue. The colour is slightly
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204 darker than background so the amino acid symbol remains visible. </em></li>
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205 <li><strong>Show Gaps<br>
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206 </strong><em>When this is selected, gap characters will be displayed as
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207 "." or "-". If unselected, then gap characters will
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208 appear as blank spaces. <br>
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209 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.</em></li>
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210 <li><strong>Show Annotations<br>
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211 </strong><em>If this is selected the "Annotation Panel" will
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212 be displayed below the alignment. The default setting is to display the
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213 conservation calculation, quality calculation and consensus values as
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214 bar charts. </em></li>
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215 <li><strong>Fetch Sequence Features<br>
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216 </strong><em>If the sequence names are Swissprot entries Jalview will
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217 use the names to retrieve <a href="../features/seqfeatures.html">sequence
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218 features</a> from the EBI. Features which are 1 residue in length are
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219 coloured red, sequences longer than 1 residue are coloured blue. Move
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220 the mouse over a coloured feature to display the details of the feature.
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222 Note: The retrieved information will update the sequence start and end
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223 labels if they are incorrect. </em></li>
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224 <li><strong>Show Sequence Features</strong><br><em>Show or
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225 hide sequence features on this alignment.</em></li>
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226 <li><strong>Seqence Feature Settings...</strong><em><br>
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227 <em>Control the colour and display of sequence features on the
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229 href="../features/featuresettings.html">Sequence Feature Settings</a>.</em><br>
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231 <li><strong><a href="../features/overview.html">Overview Window</a><br>
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232 </strong><em>A scaled version of the alignment will be displayed in a
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233 small window. A red box will indicate the currently visible area of the
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234 alignment. Move the visible region using the mouse. </em><strong> </strong></li>
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237 <li><strong>Colour</strong>
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239 <li><strong>Apply Colour To All Groups<br>
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240 </strong><em>If this is selected, any changes made to the background colour
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241 will be applied to all currently defined groups.</em></li>
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242 <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage
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243 Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,
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244 Turn Propensity, Buried Index, Nucleotide, User Defined<br>
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245 </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
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246 a description of all colour schemes.</em></li>
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247 <li><strong>By Conservation<br>
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248 </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
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249 by Conservation</a>.</em></li>
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250 <li><strong>Modify Conservation Threshold<br>
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251 </strong><em>Use this to display the conservation threshold slider window.
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252 Useful if the window has been closed, or if the 'by conservation' option
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253 appears to be doing nothing!</em></li>
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254 <li><strong>Above Identity Threshold<br>
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255 </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage
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256 Identity</a></em><strong>.</strong></li>
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257 <li><strong>Modify Identity Threshold<br>
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258 </strong><em>Use this to set the threshold value for colouring above Identity.
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259 Useful if the window has been closed. <br>
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261 <li><strong>By Annotation</strong><br>
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262 <em>Colours the alignment on a per-column value from a specified annotation.
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263 See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>
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267 <li><strong>Calculate</strong>
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271 <li><strong>by ID</strong><em><br>
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272 This will sort the sequences according to sequence name. If the sort
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273 is repeated, the order of the sorted sequences will be inverted. </em></li>
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274 <li><strong>by Group</strong><strong><br>
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275 </strong><em>This will sort the sequences according to sequence name.
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276 If the sort is repeated, the order of the sorted sequences will be
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277 inverted. </em><strong></strong></li>
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278 <li><strong>by Pairwise Identity<br>
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279 </strong><em>This will sort the selected sequences by their percentage
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280 identity to the consensus sequence. The most similar sequence is put
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281 at the top. </em></li>
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282 <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will
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283 have some additional options if you have just done a multiple alignment
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284 calculation, or opened a tree viewer window.</em></li>
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287 <li><strong>Calculate Tree </strong> <br>
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288 <em>Functions for calculating trees on the alignment or the currently
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289 selected region. See <a
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290 href="../calculations/tree.html">calculating trees</a>.</em>
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292 <li><strong>Average Distance Using % Identity</strong></li>
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293 <li><strong>Neighbour Joining Using % Identity</strong></li>
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294 <li><strong>Average Distance Using Blosum62</strong></li>
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295 <li><strong>Neighbour Joining Using Blosum62</strong></li>
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298 <li><strong>Pairwise Alignments</strong><br>
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299 <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise
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300 alignments</a>.</em></li>
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301 <li><strong>Principal Component Analysis</strong><br>
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302 <em>Shows a spatial clustering of the sequences based on the BLOSUM62
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303 scores in the alignment. See <a href="../calculations/pca.html">Principal
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304 Component Analysis</a>.</em> </li>
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305 <li><strong>Translate cDNA</strong><br>
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306 <em>If you are viewing a cDNA alignment a very simple translation service
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307 is available. The translation ignores all gaps in the cDNA sequences.
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312 <li><strong>Web Service<br>
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313 </strong> <em>Selecting one of the following menu items starts a remote service
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314 on compute facilities at the University of Dundee. You need a continuous network
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315 connection in order to use these services through Jalview. </em>
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317 <li><strong>Alignment </strong>
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319 <li><strong>ClustalW Multiple Sequence Alignment</strong><br>
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320 <em> Submits all, or just the currently selected sequences for alignment
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321 with clustal W.</em></li>
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322 <li><strong>ClustalW Multiple Sequence Alignment Realign</strong><br>
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323 <em> Submits the alignment or currently selected region for re-alignment
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324 with clustal W. Use this if you have added some new sequences to an
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325 existing alignment.</em></li>
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326 <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>
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327 <em> Submits all, or jut the currently selected sequences for alignment
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328 using Muscle. Do not use this if you are working with nucleic acid
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329 sequences.</em></li>
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332 <li><strong>Secondary Structure Prediction</strong>
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334 <li><strong>JPred Secondary Structure Prediction</strong><br>
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335 <em>Secondary structure prediction by network consensus. The behaviour
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336 of this calculation depends on the current selection: </em></li>
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337 <li><em>If nothing is selected, and the displayed sequences appear to
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338 be aligned, then a JNet prediction will be run for the first sequence
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339 in the alignment, using the current alignment. Otherwise the first
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340 sequence will be submitted for prediction. </em></li>
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341 <li><em>If just one sequence (or a region on one sequence) has been
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342 selected, it will be submitted to the automatic JNet prediction server
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343 for homolog detection and prediction. </em></li>
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344 <li><em>If a set of sequences are selected, and they appear to be aligned,
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345 then the alignment will be used for a Jnet prediction on the <strong>first</strong>
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346 sequence selected in the set (that is, the one that was first clicked
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git://source.jalview.org / jalview.git / blob