Who is Who in Phylogenetic Networks

Publication no #2410   Type :   Html | Bib | Both

Created: 2014-09-02 16:29:48

2410 Zhi-Zhong Chen, Fei Deng and Lusheng Wang. Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers. In TCBB, Vol. 9(5):1515-1528, 2012. Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction. Note: http://www.cs.cityu.edu.hk/~lwang/research/tcbb2012c.pdf.         Toggle abstract "We give a fixed-parameter algorithm for the problem of enumerating all minimum-cost LCA-reconciliations involving gene duplications, gene losses, and lateral gene transfers (LGTs) for a given species tree S and a given gene tree G. Our algorithm can work for the weighted version of the problem, where the costs of a gene duplication, a gene loss, and an LGT are left to the user's discretion. The algorithm runs in O(m+3 k/c n) time, where m is the number of vertices in S, n is the number of vertices in G, c is the smaller between a gene duplication cost and an LGT cost, and k is the minimum cost of an LCA-reconciliation between S and G. The time complexity is indeed better if the cost of a gene loss is greater than 0. In particular, when the cost of a gene loss is at least 0.614c, the running time of the algorithm is O(m+2.78 k/cn). © 2004-2012 IEEE." @Article{CDW2012,       AUTHOR = {Chen, Zhi-Zhong and Deng, Fei and Wang, Lusheng},       TITLE = {Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers},       YEAR = {2012},       JOURNAL = {TCBB},       VOLUME = {9},       NUMBER = {5},       PAGES = {1515-1528},       URL = {http://dx.doi.org/10.1109/TCBB.2012.79},       NOTE = {http://www.cs.cityu.edu.hk/~lwang/research/tcbb2012c.pdf},       KEYWORDS = {duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction} }