X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Ftree.html;h=47cac5b935e7107eff9c4b9c67bde4115048650a;hb=50b746c8bfb7cd8febdf438e6dc616687684364e;hp=5a014bbca0236e118a66ba2b8bd1368536f8c94f;hpb=3ec000e099e35b359996b824aabeaee632628deb;p=jalview.git diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index 5a014bb..47cac5b 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -3,9 +3,10 @@

Calculation of trees from alignments

Trees are calculated on either the complete alignment, or just the -currently selected group of sequences. There are four different -calculations, using one of two distance measures and constructing the -tree from one of two algorithms : +currently selected group of sequences, using the functions in the +Calculate→Calculate tree submenu. There are +four different calculations, using one of two distance measures and +constructing the tree from one of two algorithms :

Distance Measures

Trees are calculated on the basis of a measure of similarity @@ -40,9 +41,10 @@ phylogenetic tree construction, and may fail on very large alignments.

A newly calculated tree will be displayed in a new tree viewing window. In -addition, a new entry with the same tree viewer window name will be added in the Sort -menu so that the alignment can be reordered to reflect the ordering of -the leafs of the tree.

+addition, a new entry with the same tree viewer window name will be added in the Sort +menu so that the alignment can be reordered to reflect the ordering of +the leafs of the tree. If the tree was calculated on a selected region +of the alignment, then the title of the tree view will reflect this.

External Sources for Phylogenetic Trees

A number of programs exist for the reliable construction of