When a tree has been calculated from an alignment, or imported via a
file or web service it is displayed by Jalview's tree viewing
window. Trees can be rearranged, used to select sequences and groups
- in the associated alignment, saved in newick format or exported as an
+ in the associated alignment, saved in Newick format or exported as an
image or postscript file.</p>
<p>
Selecting sequence ids at the leaves of the tree selects the
<p>
Clicking anywhere along the extent of the tree (but not on a leaf or
internal node) defines a tree 'partition', by cutting every branch
- of the tree spanning the depth where the mouse-click occured. Groups
+ of the tree spanning the depth where the mouse-click occurred. Groups
are created containing sequences at the leaves of each connected
- subtree. These groups are each given a different colour, which are
+ sub tree. These groups are each given a different colour, which are
reflected in other windows in the same way as if the sequence ids
were selected, and can be edited in the same way as user defined
sequence groups.
</p>
-<p>Tree partitions are useful for comparing clusterings produced by
+<p>Tree partitions are useful for comparing clusters produced by
different methods and measures. They are also an effective way of
identifying specific patterns of conservation and mutation
corresponding to the overall phylogenetic structure, when combined
lengths, which correspond to the distance measure used to construct
the tree. Tree imported from outside may also contain bootstrap information,
or additional leaves from sequences not present in the associated
-alignment.
+alignment.
</p>
<p>The view menu contains options controlling the way a tree is
rendered and labelled:</p>
git://source.jalview.org / jalview.git / blobdiff