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» Optimal phylogenetic reconstruction
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BMCBI
2008
125views more  BMCBI 2008»
14 years 9 months ago
A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions
Background: Due to recent progress in genome sequencing, more and more data for phylogenetic reconstruction based on rearrangement distances between genomes become available. Howe...
Martin Bader, Mohamed Ibrahim Abouelhoda, Enno Ohl...
86
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JAR
2007
72views more  JAR 2007»
14 years 9 months ago
Inferring Phylogenetic Trees Using Answer Set Programming
We describe the reconstruction of a phylogeny for a set of taxa, with a character-based cladistics approach, in a declarative knowledge representation formalism, and show how to u...
Daniel R. Brooks, Esra Erdem, Selim T. Erdogan, Ja...
BMCBI
2007
162views more  BMCBI 2007»
14 years 9 months ago
Three-Dimensional Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption w
Background: Construction and interpretation of phylogenetic trees has been a major research topic for understanding the evolution of genes. Increases in sequence data and complexi...
Namshin Kim, Christopher Lee
JBI
2006
14 years 9 months ago
Missing data and the design of phylogenetic analyses
Concerns about the deleterious effects of missing data may often determine which characters and taxa are included in phylogenetic analyses. For example, researchers may exclude ta...
John J. Wiens
BMCBI
2007
147views more  BMCBI 2007»
14 years 9 months ago
MaxAlign: maximizing usable data in an alignment
Background: The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for ...
Rodrigo Gouveia-Oliveira, Peter Wad Sackett, Ander...