X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Ftree.html;h=038020fc33696d690251f5bb50d30a0a269c4d44;hb=refs%2Ftags%2FRelease_2_9_0b2;hp=946037848b64fdf0a0c8ad4100753cabf0a777c1;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index 9460378..038020f 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -1,83 +1,128 @@ -
Calculation of trees from alignments
-Trees are calculated on either the complete alignment, or just the -currently selected group of sequences, using the functions in the -Calculate→Calculate tree submenu. -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.
++ Calculation of trees from alignments +
++ Trees are calculated on either the complete alignment, or just the + currently selected group of sequences, using the functions in the Calculate→Calculate + tree submenu. 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 : +
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. +
+ 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.