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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+
+Tree Calculation
+
+
+
+ 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 :
+
+ - PID
The percentage identity
+ between the two sequences at each aligned position.
+
+ - PID = Number of equivalent aligned non-gap symbols *
+ 100 / Smallest number of non-gap positions in either of both
+ sequences
This is essentially the 'number of
+ identical bases (or residues) per 100 base pairs (or
+ residues)'.
+
+
+ - BLOSUM62, PAM250, DNA
These options
+ use one of the available substitution matrices to compute a sum of
+ scores for the residue pairs at each aligned position.
+
+ - Sequence Feature Similarity
Trees
+ are constructed from a distance matrix formed from Jaccard
+ distances between sequence features observed at each column of the
+ alignment.
+
+ - Similarity at column i = (Total number of
+ features displayed - Sum of number of features in common at i)
+
Similarities are summed over all columns and divided by
+ the number of columns.
Since the total number of
+ feature types is constant over all columns of the alignment,
+ we do not scale the matrix, so tree distances can be
+ interpreted as the average number of features that differ over
+ all sites in the aligned region.
+
+
+
Distances are computed based on the currently displayed feature
+ types. Sequences with similar distributions of features of the
+ same type will be grouped together in trees computed with this
+ metric. This measure was introduced in Jalview 2.9
+
+
+ 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.
+
+ - UPGMA tree
UPGMA stands for
+ Unweighted Pair-Group Method using Arithmetic averages. Clusters
+ are iteratively formed and extended by finding a non-member
+ sequence with the lowest average dissimilarity over the cluster
+ members.
+
+ - Neighbour Joining tree
First
+ described in 1987 by Saitou and Nei, this method applies a greedy
+ algorithm to find the tree with the shortest branch lengths.
+ This method, as implemented in Jalview, is considerably more
+ expensive than UPGMA.
+
+
+ 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.
+
+
+
+
+