The ultrametric constraint:

The ultrametric constraint was rst proposed in [GPSW03] within the

context of supertreeconstruction [BE04], and was implemented using toolkit
primitives. We review this encodingand show that in most constraint toolkits
this is inecient in terms of both space and time.This motivates the creation
of a specialised ultrametric propagator over three variables, thatmaintains
the ultrametric property over the bounds of those variables. This is presented
interms of its propagation methods. This is then extended to a specialised
propagator thatmaintains the ultrametric property on a symmetric matrix of
variables.
Previous work on the ultrametric constraint: First, we start with a denition
of the ultrametric constraint.
Denition : An ultrametric constraint on three variables (henceforth, Um-3)
x, y and z
constrains them such that:
(x > y = z) (y > x = z) (z > x = y) (x = y = z) (1)
This constraint ensures that there is a tie for the least element of the three,
i.e., eitherall three are the same, or two are the same and the other is greater.
The constraint wasproposed by [GPSW03, Pro06] and was implemented as a
literal translation of equation 1using toolkit primitives. Evidence obtained
from the JChoco, ECLiPSe and ILog constraint programming toolkits shows
that no propagation is done to lower bounds by thiscombination of primitive
constraints. This is a due to the disjunctive constraints. In manyconstraint
programming toolkits propagation on disjunctive constraints is delayed until
allbut one of the disjuncts is disentailed, i.e., delayed-disjunction consistency
is used [HSD98].Consequently, in the above encoding of the ultrametric
constraint a non-ultrametric instantiation can occur. Consider the case for
three variables: x {1, 2, 3}, y {2, 3} andz {3}. The domains of the
variables are already at a xed point with respect to delayeddisjunction
consistency and a search process can instantiate these variables and fail
(byassigning x the value 1). As we shall see later, nding a solution to the
supertree problem using toolkit constraints can result in a backtracking
search. Of course, higher levelsof consistency would overcome this, such as
constructive-disjunction consistency [HSD98],singleton arc-consistency
[DB97] or the ltering algorithm of [Lho03]. However, the cost ofthese is
greater in the average case than delayed-disjunction, preventing their use in

toolkits. In fact for the Um-3 constraint it is especially unfortunate that the
lower bounds maynot be trimmed properly.

Minimum Ultrametric Trees:

An edge-weighted tree is called ultrametric if the distances from the root to all
the leaves in the tree are equal. For an n by n distance matrix M, the minimum
ultrametric tree for M is an ultrametric tree T = (V, E, w) with leaf set {1,..., n}
such that dT(i, j) M[i, j] for all i, j and eEw(e) is minimum, where dT(i, j) is
the distance between i and j on T. Constructing minimum ultrametric trees from
distance matrices is an important problem in computational biology. In this
paper, we examine its computational complexity and approximability. When the
distances satisfy the triangle inequality, we show that the minimum ultrametric
tree problem can be approximated in polynomial time with error ratio 1.5(1 +
log n), where n is the number of species. We also develop an efficient branchand-bound algorithm for constructing the minimum ultrametric tree for both
metric and non-metric inputs. The experimental results show that it can find an
optimal solution for 25 species within reasonable time, while, to the best of our
knowledge, there is no report of algorithms solving the problem even for 12
species.
Additive trees:

A generalization of ultrametric trees are additive trees. Remind that in

an ultrametric tree, the number of mutations was assumed to be proportional to
the temporal distance of a node to the ancestor and it was also assumed that the
mutations took place with the same rate in all paths. Thus an ultramaetric tree is
assigned a root and the distance from the root to a leave is constant. But it's a fact,
that the evolutionary clock is running differently for different species and even for
different regions i.e. in a protein sequence. An unrooted phylogenetic tree is a
reflection of our ignorance as to where the common ancestor lies. All nodes of
an additive tree except for the leaves have degree three, an additive tree is
therefore an unrooted binary tree.

Definition: The additional requirement for an additive metric is:

An additive tree also is characterized by the four point condition:

Any 4 points can be renamed such that

The tree construction from an additive metric works by

successive insertion. There is exactly one tree topology that
allows for realization of an additive metric.