<mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>
<mapID target="calcs.alstrconsensus" url="html/calculations/structureconsensus.html"/>
<mapID target="calcs.consensus" url="html/calculations/consensus.html"/>
+ <mapID target="calcs.dialog" url="html/calculations/calculations.html"/>
<mapID target="nucleicAcids" url="html/na/index.html"/>
<tocitem text="Jalview Documentation" target="home" expand="true">
<tocitem text="What's new" target="new" expand="true">
<tocitem text="Latest Release Notes" target="release"/>
+ <tocitem text="Calculations Dialog" target="calcs.dialog"/>
<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
<tocitem text="Custom Colourschemes in Groovy" target="groovy.colours"/>
<tocitem text="Omit hidden regions in Overview" target="overview"/>
<tocitem text="Calculations" expand="false">
<tocitem text="Sorting alignments" target="sorting" />
- <tocitem text="Calculating trees" target="trees" />
- <tocitem text="Principal Component Analysis" target="pca" />
+ <tocitem text="Trees and PCA" target="calcs.dialog" expand="false">
+ <tocitem text="Calculating trees" target="trees" />
+ <tocitem text="Principal Component Analysis" target="pca" />
+ </tocitem>
<tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
<tocitem text="Pairwise Alignments" target="pairwise" />
<tocitem text="Remove Redundancy" target="redundancy" />
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>The Alignment Calculations Dialog</title>
+</head>
+<body>
+ <p>
+ <strong>The Alignment Calculations Dialog</strong>
+ </p>
+ <img
+ alt="Alignment Calculations dialog box - opened via Calculations->Tree or PCA..."
+ src="calculatedialog.png" width="350" height="241">
+ <p>
+ The <strong>Calculations Dialog</strong> (shown above) is opened via
+ the <strong>Calculations→Calculate Tree or PCA...</strong>
+ menu entry.
+ </p>
+ <p>
+ It allows you to select the type of alignment analysis calculation (<a
+ href="pca.html">PCA</a> or <a href="tree.html">Tree</a>), and the
+ sequence similarity score model that will be used to perform the
+ analysis.
+ </p>
+ <p>
+ <strong>Adding additional score models</strong><br />Jalview can
+ import substitution matrices in both <a
+ href="http://www.genome.jp/aaindex/aaindex_help.html">AAindex</a>
+ and NCBI format (see e.g. <a
+ href="http://ftp.ncbi.nlm.nih.gov/blast/matrices/">ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/</a>).
+ In Jalview 2.10.2, the easiest way to import new models is to drag
+ the score model file onto any alignment window. See the <a
+ href="scorematrices.html">Substitution Matrices Documentation</a>
+ for more information.
+ </p>
+</body>
+</html>
<p>
<strong>Principal Component Analysis</strong>
</p>
+ <p>A principal component analysis can be performed via the
+ <a href="calculations.html">calculations dialog</a> which is accessed by selecting <strong>Calculate→Calculate
+ Tree or PCA...</strong>.</p>
<p>This calculation creates a spatial representation of the
similarities within a selected group, or all of the sequences in an
alignment. After the calculation finishes, a 3D viewer displays the
set of sequences as points in 'similarity space', and similar
sequences tend to lie near each other in the space.</p>
<p>
- <em>Caveats</em><br />The calculation is computationally expensive,
- and may fail for very large sets of sequences - usually because the
- JVM has run out of memory. A future release of Jalview will be able
- to avoid this by executing the calculation via a web service.
+ <em>Caveats</em><br />The calculation can be computationally
+ expensive, and may fail for very large sets of sequences - usually
+ because the JVM has run out of memory. However, the PCA
+ implementation in Jalview 2.10.2 employs more memory efficient
+ matrix storage structures, allowing larger PCAs to be performed.
</p>
<p>
</p>
<p>
Trees are calculated on either the complete alignment, or just the
- currently selected group of sequences, using the functions in the <strong>Calculate→Calculate
- tree</strong> submenu. Once calculated, trees are displayed in a new <a
+ currently selected group of sequences, via the <a href="calculations.html">calculations dialog</a> opened from the <strong>Calculate→Calculate
+ Tree or PCA...</strong> menu entry. Once calculated, trees are displayed in a new <a
href="../calculations/treeviewer.html">tree viewing
window</a>. There are four different calculations, using one of two
distance measures and constructing the tree from one of two
</strong><em>Selects all the sequences and residues in the
alignment. <br> Use <CTRL> and A (<APPLE>
and A on a MacOSX) to select all.
- </em></em></li>
+ </em></li>
<li><strong>Deselect All (Escape)<br>
</strong><em>Removes the current selection box (red dashed box) from
the alignment window. All selected sequences, residues and
or hide sequence features on this alignment.</em></li>
<li><strong><a
href="../features/featuresettings.html">Sequence
- Feature Settings...</a> </strong><em><br> <em>Opens the
+ Feature Settings...</a> </strong><br> <em>Opens the
Sequence Feature Settings dialog box to control the colour
and display of sequence features on the alignment, and
configure and retrieve features from DAS annotation
</strong><em>If this box is selected then the sequence names
displayed in the sequence label area will be aligned
against the left-hand edge of the alignment display,
- rather than the left-hand edge of the alignment window.
+ rather than the left-hand edge of the alignment window.</em>
</li>
<li><strong>Show Hidden Markers<br>
</strong><em>When this box is selected, positions in the
alignment where rows and columns are hidden will be
- marked by blue arrows. </li>
+ marked by blue arrows. </em></li>
<li><strong>Boxes</strong><em><br> If this is
selected the background of a residue will be coloured
using the selected background colour. Useful if used in
symbols will be rendered as a '.', highlighting
mutations in highly conserved alignments. </em></li>
- </ul></li>
</ul></li>
</ul>
viewer window.
</em><br></li>
</ul></li>
- <li><strong>Calculate Tree </strong> <br> <em>Functions
- for calculating trees on the alignment or the currently
- selected region. See <a href="../calculations/tree.html">calculating
- trees</a>.
- </em>
- <ul>
- <li><strong>Neighbour Joining Using PAM250 </strong></li>
- <li><strong>Neighbour Joining Using Sequence
- Feature Similarity</strong></li>
- <li><strong>Neighbour Joining Using Blosum62 </strong></li>
- <li><strong>Neighbour Joining Using % Identity</strong></li>
- <li><strong>Average Distance Using PAM250 </strong></li>
- <li><strong>Average Distance Using Sequence
- Feature Similarity</strong></li>
- <li><strong>Average Distance Using Blosum62</strong></li>
- <li><strong>Average Distance Using % Identity</strong></li>
- </ul> <strong>Note: Since Version 2.8.1, a number of
- additional similarity measures for tree calculation are
- provided in this menu.</strong></li>
- <li><strong>Pairwise Alignments</strong><br> <em>Applies
- Smith and Waterman algorithm to selected sequences. See <a
- href="../calculations/pairwise.html">pairwise
- alignments</a>.
+ <li><strong>Calculate Tree or PCA ...</strong><em> <br> Opens the
+ <a href="../calculations/calculations.html">calculations dialog</a> for
+ for calculating <a href="../calculations/tree.html">trees</a> or
+ <a href="../calculations/pca.html">principle component analysis
+ plots</a> on the alignment or the currently selected
+ region.
</em><br></li>
- <li><strong>Principal Component Analysis</strong><br> <em>Shows
- a spatial clustering of the sequences based on similarity
- scores calculated with the alignment. See <a
- href="../calculations/pca.html">Principal
- Component Analysis</a>.
- </em> <br></li>
- <li><strong>Extract Scores ... (optional)</strong><br> <em>This
- option is only visible if Jalview detects one or more
- white-space separated values in the description line of the
- alignment sequences.<br> When selected, these numbers are
- parsed into sequence associated annotation which can then be
- used to sort the alignment via the Sort by→Score menu.
- </em> <br></li>
- <li><strong>Autocalculate Consensus</strong><br> <em>For
+ <li><strong>Pairwise Alignments</strong><br> <em>Applies
+ Smith and Waterman algorithm to selected sequences. See <a
+ href="../calculations/pairwise.html">pairwise
+ alignments</a>.
+ </em><br></li>
+ <li><strong>Extract Scores ... (optional)</strong><br> <em>This
+ option is only visible if Jalview detects one or more
+ white-space separated values in the description line of the
+ alignment sequences.<br> When selected, these numbers are
+ parsed into sequence associated annotation which can then be
+ used to sort the alignment via the Sort by→Score menu.
+ </em> <br></li>
+ <li><strong>Autocalculate Consensus</strong><br> <em>For
large alignments it can be useful to deselect
"Autocalculate Consensus" when editing. This
prevents the sometimes lengthy calculations performed after
in Jalview 2.8.1</strong>
</li>
<li>'Standard Databases' will check sequences against
- the EBI databases plus any active DAS sequence sources<</li>
+ the EBI databases plus any active DAS sequence sources</li>
</ul> Other sub-menus allow you to pick a specific source to query
- sources are listed alphabetically according to their
nickname.
window.
</em><br></li>
</ul></li>
- <li><strong>Calculate Tree </strong> <br> <em>Functions
- for calculating trees on the alignment or the currently selected
- region. See <a href="../calculations/tree.html">calculating
- trees</a>.
- </em>
- <ul>
- <li><strong>Neighbour Joining Using PAM250<br>
- </strong></li>
- <li><strong>Neighbour Joining Using Sequence
- Feature Similarity</strong></li>
- <li><strong>Neighbour Joining Using Blosum62<br>
- </strong></li>
- <li><strong>Neighbour Joining Using % Identity</strong></li>
- <li><strong>Average Distance Using PAM250<br>
- </strong></li>
- <li><strong>Average Distance Using Sequence
- Feature Similarity</strong></li>
- <li><strong>Average Distance Using Blosum62</strong></li>
- <li><strong>Average Distance Using % Identity</strong></li>
- </ul></li>
+ <li><strong>Calculate Tree or PCA ...</strong> <br> <em>Opens the
+ <a href="../calculations/calculations.html">calculations dialog</a> for
+ for calculating <a href="../calculations/tree.html">trees</a> or
+ <a href="../calculations/pca.html">principle component analysis
+ plots</a> on the alignment or the currently selected
+ region.
+ </em><br>
+ </li>
<li><strong>Pairwise Alignments</strong><br> <em>Applies
Smith and Waterman algorithm to selected sequences. See <a
href="../calculations/pairwise.html">pairwise
alignments</a>.
</em><br></li>
- <li><strong>Principal Component Analysis</strong><br> <em>Shows
- a spatial clustering of the sequences based on similarity scores
- calculated over the alignment.. See <a
- href="../calculations/pca.html">Principal Component
- Analysis</a>.
- </em> <br></li>
<li><strong>Extract Scores ... (optional)</strong><br> <em>This
option is only visible if Jalview detects one or more
white-space separated values in the description line of the
</ul>
</li>
<li>
+ <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
+ a calculation dialog box
+ </li>
+ <li>
<!-- JAL-2360,JAL-2371, -->More robust colours and shader
model for alignments and groups
</li>
git://source.jalview.org / jalview.git / commitdiff
