<body>\r
<p><strong>Calculation of trees from alignments</strong></p>\r
<p>Trees are calculated on either the complete alignment, or just the\r
-currently selected group of sequences. There are four different\r
-calculations, using one of two distance measures and constructing the\r
-tree from one of two algorithms :\r
+currently selected group of sequences, using the functions in the\r
+<strong>Calculate→Calculate tree</strong> submenu. There are\r
+four different calculations, using one of two distance measures and\r
+constructing the tree from one of two algorithms :\r
</p>\r
<p><strong>Distance Measures</strong></p>\r
<p>Trees are calculated on the basis of a measure of similarity\r
href="../calculations/treeviewer.html">tree viewing window</a>. In\r
addition, a new entry with the same tree viewer window name will be added in the <a href="../calculations/sort.html">Sort\r
menu</a> so that the alignment can be reordered to reflect the ordering of\r
-the leafs of the tree.</p>\r
+the leafs of the tree. If the tree was calculated on a selected region\r
+of the alignment, then the title of the tree view will reflect this.</p>\r
\r
<p><strong>External Sources for Phylogenetic Trees</strong></p>\r
<p>A number of programs exist for the reliable construction of\r
git://source.jalview.org / jalview.git / blobdiff