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As any cluster method, UPGMA (unweighted
pair-group method of analysis) performs the structure of a set
of some homogeneous elements (in our case alignment is a set
of amino acid sequences). Like UPGMA (carrying out an
unweighted clusterisation), this method is based on consecutive
joining of elements into clusters and then clusters and (or)
separate elements together. Usually cluster methods are used for
constructing phylogenetic trees. But WPGMA has its own specificity:
working with clusters, it estimates weights of every cluster.
Moreover, weights of all sequences in these clusters are also
calculated. This statement is also right for the last cluster
(containing all objects of the set) - thus, there is an opportunity
of using WPGMA for weighting sequences in alignment.
While gathering objects, WPGMA constructs a tree. This tree represents phylogeny rather reliably (WPGMA is based on the same principles with UPGMA, which is widely used for phylogeny reconstruction). SVETKA can analyse alignments together with any assigned tree (of course, sets presented in the tree and in the alignment should coincide - but the topology of this tree can be arbitrary). Despite this, assignment of tree topology (by citing tree bracket scheme) is not necessary. In the case when only alignment is given, the program uses WPGMA-constructed tree (as default). The tree is then presented in all diagrams ane web-pages, further calculations (definition of supporing positions, calculations of branch parameters) are made for this tree.
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