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Search results for: MATCHING SPLIT DISTANCE
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Matching Split Distance for Unrooted Binary Phylogenetic Trees
PublicationRekonstrukcja drzew ewolucji jest jednym z głównych celów w bioinformatyce. Drzewa filogenetyczne reprezentuje historię ewolucji i związki pokrewieństwa między różnymi gatunkami. W pracy proponujemy nową ogólną metodę określania odległości między nieukorzenionymi drzewami filogenetycznymi, szczególnie użyteczną dla dużych zbiorów gatunków. Następnie podajemy szczegółowe własności jednej metryki określonej przy użyciu tej metody...
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Matching Split Distance for Unrooted Binary Phylogenetic Trees
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Comparing Arbitrary Unrooted Phylogenetic Trees Using Generalized Matching Split Distance
PublicationIn the paper, we describe a method for comparing arbitrary, not necessary fully resolved, unrooted phylogenetic trees. Proposed method is based on finding a minimum weight matching in bipartite graphs and can be regarded as a generalization of well-known Robinson-Foulds distance. We present some properties and advantages of the new distance. We also investigate some properties of presented distance in a common biological problem...
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On a matching distance between rooted phylogenetic trees
PublicationThe Robinson–Foulds (RF) distance is the most popular method of evaluating the dissimilarity between phylogenetic trees. In this paper, we define and explore in detail properties of the Matching Cluster (MC) distance, which can be regarded as a refinement of the RF metric for rooted trees. Similarly to RF, MC operates on clusters of compared trees, but the distance evaluation is more complex. Using the graph theoretic approach...
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Optimal backbone coloring of split graphs with matching backbones
PublicationFor a graph G with a given subgraph H, the backbone coloring is defined as the mapping c: V(G) -> N+ such that |c(u)-c(v)| >= 2 for each edge uv \in E(H) and |c(u)-c(v)| >= 1 for each edge uv \in E(G). The backbone chromatic number BBC(G;H) is the smallest integer k such that there exists a backbone coloring with max c(V(G)) = k. In this paper, we present the algorithm for the backbone coloring of split graphs with matching backbone.
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Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions
PublicationAbility to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in...
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Generalization of Phylogenetic Matching Metrics with Experimental Tests of Practical Advantages
PublicationThe ability to quantify a dissimilarity of different phylogenetic trees is required in various types of phylogenetic studies, for example, such metrics are used to assess the quality of phylogeny construction methods and to define optimization criteria in supertree building algorithms. In this article, starting from the already described concept of matching metrics, we define three new metrics for rooted phylogenetic trees. One...
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Distance measurement by the low coherent interferometer
Open Research DataThe obtained data was acquired by the interferometric fiber-optic sensor of distance. The setup was constructed of a broadband light source working at the central wavelength of 1560 nm, an optical spectrum analyzer and a fiber-optic 2x1 coupler (with the power split 50:50). All elements were connected by standard single-mode optical fibers. The measurement...
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Towards increasing F-measure of approximate string matching in O(1) complexity
PublicationThe paper analyzes existing approaches for approximate string matching based on linear search with Levenshtein distance, AllScan and CPMerge algorithms using cosine, Jaccard and Dice distance measures. The methods are presented and compared to our approach that improves indexing time using Locally Sensitive Hashing. Advantages and drawbacks of the methods are identified based on theoretical considerations as well as empirical evaluations...
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Rendezvous of Distance-Aware Mobile Agents in Unknown Graphs
PublicationWe study the problem of rendezvous of two mobile agents starting at distinct locations in an unknown graph. The agents have distinct labels and walk in synchronous steps. However the graph is unlabelled and the agents have no means of marking the nodes of the graph and cannot communicate with or see each other until they meet at a node. When the graph is very large we want the time to rendezvous to be independent of the graph size...