Comparison of weighted labelled trees

Robinson, D. F.; Foulds, L. R.

doi:10.1007/bfb0102690

Cited by 138 publications

(115 citation statements)

References 3 publications

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“…The topological accuracy of these various methods was measured on the 5,000 data sets (without rate heterogeneity) by the standard Robinson and Foulds (1979) distance between the inferred tree and the true tree. This distance corresponds to the proportion of internal branches that are found in one tree and not in the other one.…”

Section: Topological Accuracymentioning

confidence: 99%

SPMM: estimating infection duration of multivariant HIV-1 infections

et al. 2015

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Abstract.-The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximumlikelihood principle, which clearly satisfies these requirements. The core of this method is a simple hill-climbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distance-based method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment of the topology and branch lengths, only a few iterations are sufficient to reach an optimum. We used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches. The reduction of computing time is dramatic in comparison with other maximum-likelihood packages, while the likelihood maximization ability tends to be higher. For example, only 12 min were required on a standard personal computer to analyze a data set consisting of 500 rbcL sequences with 1,428 base pairs from plant plastids, thus reaching a speed of the same order as some popular distance-based and parsimony algorithms. This new method is implemented in the PHYML program, which is freely available on our web page:

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Section: Topological Accuracymentioning

confidence: 99%

SPMM: estimating infection duration of multivariant HIV-1 infections

et al. 2015

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“…Both topologies were also compared using the Robinson and Foulds (RF;1979) distance, which is the number of branches (bipartitions) that belong to one tree but not to the other. When different topologies are found, one should prefer the one with best likelihood value or best AIC (or similar criterion) value, when evolutionary models used for tree inference involve different numbers of parameters.…”

Section: Comparison Criteria and Methodsmentioning

confidence: 99%

Modeling Protein Evolution with Several Amino Acid Replacement Matrices Depending on Site Rates

Dang

Gascuel

2012

Molecular Biology and Evolution

206

173

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Most protein substitution models use a single amino acid replacement matrix summarizing the biochemical properties of amino acids. However, site evolution is highly heterogeneous and depends on many factors that influence the substitution patterns. In this paper, we investigate the use of different substitution matrices for different site evolutionary rates. Indeed, the variability of evolutionary rates corresponds to one of the most apparent heterogeneity factors among sites, and there is no reason to assume that the substitution patterns remain identical regardless of the evolutionary rate. We first introduce LG4M, which is composed of four matrices, each corresponding to one discrete gamma rate category (of four). These matrices differ in their amino acid equilibrium distributions and in their exchangeabilities, contrary to the standard gamma model where only the global rate differs from one category to another. Next, we present LG4X, which also uses four different matrices, but leaves aside the gamma distribution and follows a distribution-free scheme for the site rates. All these matrices are estimated from a very large alignment database, and our two models are tested using a large sample of independent alignments. Detailed analysis of resulting matrices and models shows the complexity of amino acid substitutions and the advantage of flexible models such as LG4M and LG4X. Both significantly outperform single-matrix models, providing gains of dozens to hundreds of log-likelihood units for most data sets. LG4X obtains substantial gains compared with LG4M, thanks to its distribution-free scheme for site rates. Since LG4M and LG4X display such advantages but require the same memory space and have comparable running times to standard models, we believe that LG4M and LG4X are relevant alternatives to single replacement matrices. Our models, data, and software are available from http://www.atgc-montpellier.fr/models/lg4x.

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“…For measuring the similarity / difference between trees, several distance measures have been proposed [9], e.g. the symmetric difference metric [23], the nearest-neighbor interchange metric [29], the subtree transfer distance [2], the Robinson and Foulds (RF) metric [24], and the quartet metric [11,6].…”

Section: Introductionmentioning

confidence: 99%

Efficient Algorithms for Descendent Subtrees Comparison of Phylogenetic Trees with Applications to Co-evolutionary Classifications in Bacterial Genome

Lin

Hsu

2003

Algorithms and Computation

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Abstract. A phylogenetic tree is a rooted tree with unbounded degree such that each leaf node is uniquely labelled from 1 to n. The descendent subtree of of a phylogenetic tree T is the subtree composed by all edges and nodes of T descending from a vertex. Given a set of phylogenetic trees, we present linear time algorithms for finding all leaf-agree descendent subtrees as well as all isomorphic descendent subtrees. The normalized cluster distance, d(A, B), of two sets is defined by d(A, B) = ∆(A, B)/(|A| + |B|), where ∆(A, B)denotes the symmetric set difference of two sets. We show that computing all pairs normalized cluster distances between descendent subtrees of two phylogenetic trees can be done in O(n 2 ) time. Since the total size of the outputs will be Θ(n 2 ), the algorithm is thus computationally optimal. A nearest subtree of a subset of leaves is such a descendent subtree that has the smallest normalized cluster distance to these leaves. Here we show that finding nearest subtrees for a collection of pairwise disjointed subsets of leaves can be done in O(n) time. Several applications of these algorithms in areas of bioinformatics is considered. Among them, we discuss the 2CS (Two component systems) functional analysis and classifications on bacterial genome.

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Comparison of weighted labelled trees

Cited by 138 publications

References 3 publications

SPMM: estimating infection duration of multivariant HIV-1 infections

SPMM: estimating infection duration of multivariant HIV-1 infections

Modeling Protein Evolution with Several Amino Acid Replacement Matrices Depending on Site Rates

Efficient Algorithms for Descendent Subtrees Comparison of Phylogenetic Trees with Applications to Co-evolutionary Classifications in Bacterial Genome

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