X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Ftree.html;h=47cac5b935e7107eff9c4b9c67bde4115048650a;hb=2a436b9052affcfeb6f3748a40de53f6b8a7e9ef;hp=c767bf275713cb0582563956f8f7a3a0bec823d7;hpb=8ee7a0f79f6da26d5011c60a80226d6994733cab;p=jalview.git diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index c767bf2..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 treeviewer 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