ordering and the redundancy calculation help description.
\r
<mapID target="io" url="html/io/index.html"/>\r
<mapID target="edit" url="html/editing/index.html"/>\r
- \r
+\r
<mapID target="calculations" url="html/calculations/index.html"/>\r
<mapID target="trees" url="html/calculations/tree.html"/>\r
+ <mapID target="sorting" url="html/calculations/sorting.html"/>\r
<mapID target="pca" url="html/calculations/pca.html"/>\r
<mapID target="pairwise" url="html/calculations/pairwise.html"/>\r
<mapID target="redundancy" url="html/calculations/redundancy.html"/>\r
<tocitem text="By conservation" target="colours.conservation"/>\r
</tocitem>\r
<tocitem text="Calculations" target="calculations" expand="false">\r
- <tocitem text="Calculating trees" target="trees"/>\r
+ <tocitem text="Sorting alignments" target="sorting"/>\r
+ <tocitem text="Calculating trees" target="trees"/>\r
<tocitem text="Principal Component Analysis" target="pca"/>\r
<tocitem text="Pairwise Alignments" target="pairwise"/>\r
<tocitem text="Remove Redundancy" target="redundancy"/>\r
<body>\r
<p><strong>Removing redundancy</strong></p>\r
<p>Selecting this option brings up a window asking you to select a threshold.\r
- If the percentage identity between two sequences exceeds this value one of the\r
+ If the percentage identity between two sequences (based on the\r
+ current alignment) exceeds this value one of the\r
sequences (the shorter) is discarded. The redundancy calculation is done when\r
- the Apply button is pressed. For large numbers of sequences this can take a\r
- long time as all pairs have to be compared. </p>\r
+ the Apply button is pressed, and the undo button recovers the\r
+ original set or any previously calculated subset. The detection of\r
+ redundant sequences involves a pairwise comparison of all the\r
+ sequences, so you may have to wait a few moments when applying this to\r
+ large sequence sets.</p>\r
</body>\r
</html>\r
<p>Places sequences in the same group adjacent to eachother.</p><p>
</li>
<li><p><strong>Sort by Pairwise Identity</strong></p>
-<p>Places pairs of sequences together that align with the greatest
-fraction of conserved residues.
+<p>Sequences are ordered by decreasing fraction of conserved residues
+with respect to the first sequence in the alignment.
</p><p>
</li>
<li><p><strong>Sort by Tree Order</strong></p>
alignments by some measure of sequence identity.<br>
If the current alignment has been generated by one of Jalview's
alignment web services, the alignment ordering can be recovered by
-its corresponding entry in the Sort menu.
-</p><p>
+its corresponding entry in the Sort menu:
</li>
</ul>
-<p><strong>Reversing the Order</strong></p>
-<p>Selecting any item from the Sort menu will sort sequences in an
-ascending order according to the property defining the sort. If the
-same sort is re-applied, the sequences will be sorted in the inverse
-order. In the case of trees and alignment orderings, Jalview will
+<strong>Reversing the Order</strong>
+<p>If a sort is re-applied (by selecting the same menu item once again), the sequences will be sorted in the inverse
+order for that property. In the case of trees and alignment orderings, Jalview will
remember your last choice for sorting the alignment and only apply the
inverse ordering if you select the same tree or alignment ordering
item again.</p>
git://source.jalview.org / jalview.git / commitdiff