  
Ali Tofigh,
Mike Hallett and
Jens Lagergren. Simultaneous Identification of Duplications and Lateral Gene Transfers. In TCBB, Vol. 8(2):517-535, 2011.
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1109/TCBB.2010.14.
Toggle abstract
"The incongruency between a gene tree and a corresponding species tree can be attributed to evolutionary events such as gene duplication and gene loss. This paper describes a combinatorial model where so-called DTL-scenarios are used to explain the differences between a gene tree and a corresponding species tree taking into account gene duplications, gene losses, and lateral gene transfers (also known as horizontal gene transfers). The reasonable biological constraint that a lateral gene transfer may only occur between contemporary species leads to the notion of acyclic DTL-scenarios. Parsimony methods are introduced by defining appropriate optimization problems. We show that finding most parsimonious acyclic DTL-scenarios is NP-hard. However, by dropping the condition of acyclicity, the problem becomes tractable, and we provide a dynamic programming algorithm as well as a fixed-parameter tractable algorithm for finding most parsimonious DTL-scenarios. © 2011 IEEE."
@Article{THL2011,
AUTHOR = {Tofigh, Ali and Hallett, Mike and Lagergren, Jens},
TITLE = {Simultaneous Identification of Duplications and Lateral Gene Transfers},
YEAR = {2011},
JOURNAL = {TCBB},
VOLUME = {8},
NUMBER = {2},
PAGES = {517-535},
URL = {http://dx.doi.org/10.1109/TCBB.2010.14},
NOTE = { http://dx.doi.org/10.1109/TCBB.2010.14},
KEYWORDS = {duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction} } |
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