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**11 - 20**of**20**### DOI: 10.1142/S0218339010003408 WHOLE GENOME COMPARISONS REVEALS A

, 2010

"... The availability of whole genome sequences from multiple metazoan phyla is making it possible to determine their phylogeny. We have found that a sea urchin and human define a clade that excludes a tunicate, contradicting both classical and recent molecular studies that place the tunicate and vertebr ..."

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The availability of whole genome sequences from multiple metazoan phyla is making it possible to determine their phylogeny. We have found that a sea urchin and human define a clade that excludes a tunicate, contradicting both classical and recent molecular studies that place the tunicate and vertebrate in the Chordate phylum. Intriguingly, by means of a novel four taxa analysis, we have partitioned the 2000 proteins responsible for this assignment into two groups. One group, containing about 40 % of the proteins, supports the classical assemblage of the tunicate with vertebrates, while the remaining group places the tunicate outside of the chordate assemblage. The existence of these two phylogenetic groups is robustly maintained in five, six and nine taxa analyses. These results suggest that major horizontal gene transfer events occurred during the emergence of one of the metazoan phyla. The simplest explanation is that the modern tunicate (as represented by Ciona intestinalis) began as a hybrid between a primitive vertebrate and some other organism, perhaps from an extinct and unidentified protostome phylum, at a time close to but after the diversification of the chordates and echinoderms and before the lineages leading to Drosophila melanogaster and Caenorhabditis elegans diverged.

### LEVEL-K PHYLOGENETIC NETWORK CAN BE CONSTRUCTED FROM A DENSE TRIPLET SET IN POLYNOMIAL TIME THU-HIEN TO AND MICHEL HABIB

"... Abstract. Given a dense triplet set T, there arise two interesting questions [7]: Does there exists any phylogenetic network consistent with T? And if so, can we find an effective algorithm to construct one? For cases of networks of levels k = 0 or 1 or 2, these questions were answered in [1, 6, 7, ..."

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Abstract. Given a dense triplet set T, there arise two interesting questions [7]: Does there exists any phylogenetic network consistent with T? And if so, can we find an effective algorithm to construct one? For cases of networks of levels k = 0 or 1 or 2, these questions were answered in [1, 6, 7, 8, 10] with effective polynomial algorithms. For higher levels k, partial answers were recently obtained in [11] with an O(|T | k+1) time algorithm for simple networks. In this paper we give a complete answer to the general case, solving a problem of [7]. The main idea is to use a special property of SN-sets in a level-k network. As a consequence, we can also find the level-k network with the minimum number of reticulations in polynomial time. hal-00352360, version 1- 12 Jan 2009 1.

### Constructing Rooted Phylogenetic Networks from Triplets based on Height Function

"... Abstract — The problem of constructing an optimal rooted phylogenetic network from a set of rooted triplets is NP-hard. In this paper, we present a novel method called NCH, which tries to construct a rooted phylogenetic network with the minimum numberof reticulation nodes from an arbitrary set of r ..."

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Abstract — The problem of constructing an optimal rooted phylogenetic network from a set of rooted triplets is NP-hard. In this paper, we present a novel method called NCH, which tries to construct a rooted phylogenetic network with the minimum numberof reticulation nodes from an arbitrary set of rooted triplets based on the concept of the height function of a tree and a network. We report the performance of this method on simulated data.

### Constructing a Minimum-Level Phylogenetic Network from a Dense Triplet Set in Polynomial Time

, 2013

"... For a given set L of species and a set T of triplets on L, we want to construct a phylogenetic network which is consistent with T, i.e which represents all triplets of T. The level of a network is defined as the maximum number of hybrid vertices in its biconnected components. When T is dense, there ..."

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For a given set L of species and a set T of triplets on L, we want to construct a phylogenetic network which is consistent with T, i.e which represents all triplets of T. The level of a network is defined as the maximum number of hybrid vertices in its biconnected components. When T is dense, there exist polynomial time algorithms to construct level-0, 1, 2 networks [1, 9, 10, 17]. For higher levels, partial answers were obtained in [18] with a polynomial time algorithm for simple networks. In this paper, we detail the first complete answer for the general case, solving a problem proposed in [10] and [17]: for any k fixed, it is possible to construct a minimum level-k network consistent with T, if there is any, in time O(|T |k+1nb 4k3 c+1) 1.

### TripNet: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets

, 2014

"... The problem of constructing an optimal rooted phylogenetic network from an arbitrary set of rooted triplets is an NP-hard problem. In this paper, we present a heuristic algorithm called TripNet, which tries to construct a rooted phylogenetic network with the minimum number of reticulation nodes from ..."

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The problem of constructing an optimal rooted phylogenetic network from an arbitrary set of rooted triplets is an NP-hard problem. In this paper, we present a heuristic algorithm called TripNet, which tries to construct a rooted phylogenetic network with the minimum number of reticulation nodes from an arbitrary set of rooted triplets. Despite of current methods that work for dense set of rooted triplets, a key innovation is the applicability of TripNet to non-dense set of rooted triplets. We prove some theorems to clarify the performance of the algorithm. To demonstrate the efficiency of TripNet, we compared TripNet with SIMPLISTIC. It is the only available software which has the ability to return some rooted phylogenetic network consistent with a given dense set of rooted triplets. But the results show that for complex networks with high levels, the SIMPLISTIC running time increased abruptly. However in all cases TripNet outputs an appropriate rooted phylogenetic network in an acceptable time. Also we tetsed TripNet on the Yeast data. The results show that Both TripNet and optimal networks have the same clustering and TripNet produced a level-3 network which contains only one more reticulation node than the optimal network.

### unknown title

"... 1Fighting network space: it is time for an SQL-type language to filter phylogenetic networks ..."

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1Fighting network space: it is time for an SQL-type language to filter phylogenetic networks