computational biology

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computational biology

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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.

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:

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.

Any 4 points can be renamed such that

successive insertion. There is exactly one tree topology that

allows for realization of an additive metric.

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