X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Ftree.html;h=95904b6a18aa960e46a1c430fbe063c3ff7764bf;hb=ead01b555e8b1d6322cecdf7780222c73143a03a;hp=1f9317eedaa205a704eb9811b5284cf0c5848989;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index 1f9317e..95904b6 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -1,91 +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, 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 : +
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.