Abstract
The problem of constructing a minimally resolved phylogenetic supertree (i.e., a rootedtree having the smallest possible number of internal nodes) that contains all of the rooted triplets froma consistent set R is known to be NP-hard. In this article, we prove that constructing a phylogenetictree consistent with R that contains the minimum number of additional rooted triplets is also NP-hard,and develop exact, exponential-time algorithms for both problems. The new algorithms are applied toconstruct two variants of the local consensus tree; for any set S of phylogenetic trees over some leaflabel set L, this gives a minimal phylogenetic tree over L that contains every rooted triplet present in alltrees in S, where “minimal” means either having the smallest possible number of internal nodes or thesmallest possible number of rooted triplets. (The second variant generalizes the RV-II tree, introducedby Kannan et al. in 1998.) We also measure the running times and memory usage in practice of thenew algorithms for various inputs. Finally, we use our implementations to experimentally investigatethe non-optimality of Aho et al.’s well-known BUILD algorithm from 1981 when applied to the localconsensus tree problems considered here.
Highlights
Phylogenetic trees are used to describe evolutionary relationships between species [11]
A consensus tree [1, 7, 17] can be regarded as the special case of a phylogenetic supertree where all the trees that are to be combined have the same leaf label set
The BUILD algorithm [2] is a recursive, top-down algorithm that takes as input a set R of rooted triplets and a leaf label set L such that t∈R Λ(t) ⊆ L and outputs a tree T with Λ(T ) = L that is consistent with all of the rooted triplets in R, if such a tree exists; otherwise, it outputs fail
Summary
Phylogenetic trees are used to describe evolutionary relationships between species [11]. One class of supertree methods consists of the BUILD algorithm [2] and its various extensions [10, 13, 14, 18, 19, 20, 21, 24] for combining a set of rooted triplets (binary phylogenetic trees with three leaves each), e.g., inferred by the method in [9]. A consensus tree [1, 7, 17] can be regarded as the special case of a phylogenetic supertree where all the trees that are to be combined have the same leaf label set.
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