Who is Who in Phylogenetic Networks

Publications of Yuanyi Zhang     Order by:   Type | Year

Associated keywords

abstract-network explicit-network from-distances phylogenetic-network phylogeny reconstruction split split-network visualization

Article (Journal)

1 Sergey Bereg and Yuanyi Zhang. Phylogenetic Networks Based on the Molecular Clock Hypothesis. In TCBB, Vol. 3(4), 2006. Note: http://www.utdallas.edu/~yzhang/Homepage/Papers/prep-tcbb.pdf.         Toggle abstract A classical result in phylogenetic trees is that a binary phylogenetic tree adhering to the molecular clock hypothesis exists if and only if the matrix of distances between taxa is ultrametric. The ultrametric condition is very restrictive. In this paper we study phylogenetic networks that can be constructed assuming the molecular clock hypothesis. We characterize distance matrices that admit such networks for 3 and 4 taxa. We also design two algorithms for constructing networks optimizing the least-squares fit.

InProceedings

2 Sergey Bereg and Yuanyi Zhang. Phylogenetic Networks Based on the Molecular Clock Hypothesis. In BIBE05, Pages 320-323, 2005. Note: http://dx.doi.org/10.1109/BIBE.2005.46.         Toggle abstract A classical result in phylogenetic trees is that a binary phylogenetic tree adhering to the molecular clock hypothesis exists if and only if the matrix of distances between taxa is ultrametric. The ultrametric condition is very restrictive. In this paper we study phylogenetic networks that can be constructed assuming the molecular clock hypothesis. We characterize distance matrices that admit such networks for 3 and 4 taxa. We design an efficient algorithm for a special class of phylogenetic networks that can detect the existence of a network and constructs it. © 2005 IEEE.

PhdThesis

3 Yuanyi Zhang. Optimization Algorithms for Phylogenetic Networks. PhD thesis, University of Texas at Dallas, U.S.A., 2007. Keywords: abstract network, explicit network, from distances, phylogenetic network, phylogeny, reconstruction, split, split network, visualization. Note: http://proquest.umi.com/pqdlink?did=1421626541&sid=1&Fmt=6&clientId=176295&RQT=309&VName=PQD.

Misc

4 Yuanyi Zhang, Lichen Bao and Sergey Bereg. Optimizing Split Networks. 2007. Note: UC Dallas Computer Science Technical Report UTDCS-08-07.