Split Decomposition via Graph-Labelled Trees

Author(s):  
Christophe Paul
Algorithmica ◽  
2013 ◽  
Vol 69 (4) ◽  
pp. 789-843 ◽  
Author(s):  
Emeric Gioan ◽  
Christophe Paul ◽  
Marc Tedder ◽  
Derek Corneil

2004 ◽  
Vol 46 (3) ◽  
pp. 145-152 ◽  
Author(s):  
Cecília Luiza S. Santos ◽  
Maria Anice M. Sallum ◽  
Peter G. Foster ◽  
Iray Maria Rocco

The genomic sequences of the Envelope-Non-Structural protein 1 junction region (E/NS1) of 84 DEN-1 and 22 DEN-2 isolates from Brazil were determined. Most of these strains were isolated in the period from 1995 to 2001 in endemic and regions of recent dengue transmission in São Paulo State. Sequence data for DEN-1 and DEN-2 utilized in phylogenetic and split decomposition analyses also include sequences deposited in GenBank from different regions of Brazil and of the world. Phylogenetic analyses were done using both maximum likelihood and Bayesian approaches. Results for both DEN-1 and DEN-2 data are ambiguous, and support for most tree bipartitions are generally poor, suggesting that E/NS1 region does not contain enough information for recovering phylogenetic relationships among DEN-1 and DEN-2 sequences used in this study. The network graph generated in the split decomposition analysis of DEN-1 does not show evidence of grouping sequences according to country, region and clades. While the network for DEN-2 also shows ambiguities among DEN-2 sequences, it suggests that Brazilian sequences may belong to distinct subtypes of genotype III.


2008 ◽  
Vol DMTCS Proceedings vol. AJ,... (Proceedings) ◽  
Author(s):  
Markus Kuba ◽  
Alois Panholzer

International audience We study two enumeration problems for $\textit{up-down alternating trees}$, i.e., rooted labelled trees $T$, where the labels $ v_1, v_2, v_3, \ldots$ on every path starting at the root of $T$ satisfy $v_1 < v_2 > v_3 < v_4 > \cdots$. First we consider various tree families of interest in combinatorics (such as unordered, ordered, $d$-ary and Motzkin trees) and study the number $T_n$ of different up-down alternating labelled trees of size $n$. We obtain for all tree families considered an implicit characterization of the exponential generating function $T(z)$ leading to asymptotic results of the coefficients $T_n$ for various tree families. Second we consider the particular family of up-down alternating labelled ordered trees and study the influence of such an alternating labelling to the average shape of the trees by analyzing the parameters $\textit{label of the root node}$, $\textit{degree of the root node}$ and $\textit{depth of a random node}$ in a random tree of size $n$. This leads to exact enumeration results and limiting distribution results. Nous étudions deux problèmes de dénombrement d'$\textit{arbres alternés haut-bas}$ : par définition, ce sont des arbres munis d'une racine et tels que, pour tout chemin partant de la racine, les valeurs $v_1,v_2,v_3,\ldots$ associées aux nœuds du chemin satisfont la chaîne d'inégalités $v_1 < v_2 > v_3 < v_4 > \cdots$. D'une part, nous considérons diverses familles d'arbres intéressantes du point de vue de l'analyse combinatoire (comme les arbres de Motzkin, les arbres non ordonnés, ordonnés et $d$-aires) et nous étudions pour chaque famille le nombre total $T_n$ d'arbres alternés haut-bas de taille $n$. Nous obtenons pour toutes les familles d'arbres considérées une caractérisation implicite de la fonction génératrice exponentielle $T(z)$. Cette caractérisation nous renseigne sur le comportement asymptotique des coefficients $T_n$ de plusieurs familles d'arbres. D'autre part, nous examinons le cas particulier de la famille des arbres ordonnés : nous étudions l'influence de l'étiquetage alterné haut-bas sur l'allure générale de ces arbres en analysant trois paramètres dans un arbre aléatoire (valeur de la racine, degré de la racine et profondeur d'un nœud aléatoire). Nous obtenons alors des résultats en terme de distribution limite, mais aussi de dénombrement exact.


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