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|Criteria of branch quality|
As it was repeatedly told, phylogenetic
trees consist from branches. Every branch is a set of taxons,
all branches unite in a general tree et cetera.
Firstly, one can calculate the quantity of positions, supporting some branch. I. e., those positions, which can separate sequences of the branch from other sequences in the alignment. The number of such supporting positions is marked on every branch of phylogenetic tree.
Then, every set of sequences can be simply estimated.
As the metric is introduced, we can analyse distribution of
sequences inside any set. For branch estimation two measures
- distance between this branch and another part of alignment - minimal distance between two sequences; the former sequence is inside the branch, the latter is outside the branch:
Both these measures vary in different alignments, that's why their ratio seems to be more convenient (we called it garno:
On the page, where all branches of tree are descripted, these garnos are not cited, but they are considered. Branches, which are well-separated from the other part (i.e. this ratio is considerably greater than 1 - we accepted threshold 1.15), are green-colored; those branches, for which this ratio is near to 1 (more accurately, it varies from 0.85 to 1.15), are brown-colored; the worst branches (their garno is less than 0.85), are red-colored. Besides these standard colors, two additional are used. We decided to mark very noticeable branches (those, which garnos are more than 2) by blue color. At last, some branches consist only from 1 taxon (they are usually not interesting, but nevertheless are cited) - their diameter and, thus, garno cannpt be calculated. These branches are marked by black color. Also garno can't be calculated for the branches which consist of several taxa, but extract one taxon (i.e. include all except one taxa in the tree). Such branches are also marked by black color.
Conserved positions in any aligned sequence set are
assumed to keep the majority of properties of this set. That
is why the quantity and the part of conserved positions are
the main characteristics of alignments.
Notice that, after adding different sequences, different
conserved positions could be lost. But this formula allows to
calculate only the maximal part of positions, which can be
lost after adding only one sequence. That means,
SavCons gives the lower measure of group specificity,
than it can really be.
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