X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Fcalculations%2Ftree.html;h=95904b6a18aa960e46a1c430fbe063c3ff7764bf;hb=14d7fc7b354d68634fdb65c20ace15741a5b685f;hp=5a014bbca0236e118a66ba2b8bd1368536f8c94f;hpb=3ec000e099e35b359996b824aabeaee632628deb;p=jalview.git diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index 5a014bb..95904b6 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -1,60 +1,130 @@ - -
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 : -
-Distance Measures
-Trees are calculated on the basis of a measure of similarity -between each pair of sequences in the alignment : -
Tree Construction Methods
-Jalview currently supports two kinds of agglomerative clustering -methods. These are not intended to substitute for rigorous -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.
- -External Sources for Phylogenetic Trees
-A number of programs exist for the reliable construction of - phylogenetic trees, which can cope with large numbers of sequences, - use better distance methods and can perform bootstrapping. Jalview - can read Newick - format tree files using the 'Load Associated Tree' entry of the - alignment's File menu. Sequences in the alignment will be - automatically associated to nodes in the -
- - - - + + + ++ Calculation of trees from alignments +
++ Trees are calculated on either the complete alignment, or just the + currently selected group of sequences, via the calculations dialog opened from the Calculate→Calculate + Tree or PCA... menu entry. Once calculated, trees are displayed in a new tree viewing + window. 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 + between each pair of sequences in the alignment : +
+ Tree Construction Methods +
+Jalview currently supports two kinds of agglomerative + clustering methods. These are not intended to substitute for + rigorous 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. 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 + phylogenetic trees, which can cope with large numbers of sequences, + use better distance methods and can perform bootstrapping. Jalview + can read Newick + format tree files using the 'Load Associated Tree' entry of the + alignment's File menu. Sequences in the alignment will be + automatically associated to nodes in the tree, by matching Sequence + IDs to the tree's leaf names. +
+ + + +