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BMCBI
2010
108views more  BMCBI 2010»
13 years 11 months ago
iGTP: A software package for large-scale gene tree parsimony analysis
Background: The ever-increasing wealth of genomic sequence information provides an unprecedented opportunity for large-scale phylogenetic analysis. However, species phylogeny infe...
Ruchi Chaudhary, Mukul S. Bansal, André Weh...
JCB
2007
104views more  JCB 2007»
13 years 11 months ago
Counting Coalescent Histories
Given a species tree and a gene tree, a valid coalescent history is a list of the branches of the species tree on which coalescences in the gene tree take place. I develop a recur...
Noah A. Rosenberg
BMCBI
2010
135views more  BMCBI 2010»
13 years 11 months ago
Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models
Background: Genomic data provide a wealth of new information for phylogenetic analysis. Yet making use of this data requires phylogenetic methods that can efficiently analyze extr...
Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulens...
COCOON
2006
Springer
14 years 3 months ago
Reconciling Gene Trees with Apparent Polytomies
We consider the problem of reconciling gene trees with a species tree based on the widely accepted Gene Duplication model from Goodman et al. Current algorithms that solve this pro...
Wen-Chieh Chang 0002, Oliver Eulenstein
RECOMB
2008
Springer
14 years 12 months ago
Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations
We describe algorithms to explore the space of all possible reconciliations between a gene tree and a species tree. We propose an algorithm for generating a random reconciliation, ...
Jean-Philippe Doyon, Cedric Chauve, Sylvie Hamel