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96
Voted
BMCBI
2010
135views more  BMCBI 2010»
15 years 26 days 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...
114
Voted
BMCBI
2010
112views more  BMCBI 2010»
15 years 26 days ago
A parameter-adaptive dynamic programming approach for inferring cophylogenies
Background: Coevolutionary systems like hosts and their parasites are commonly used model systems for evolutionary studies. Inferring the coevolutionary history based on given phy...
Daniel Merkle, Martin Middendorf, Nicolas Wieseke
116
Voted
BMCBI
2010
189views more  BMCBI 2010»
15 years 26 days ago
Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs
Background: Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly probl...
Vamsi Kundeti, Sanguthevar Rajasekaran, Hieu Dinh,...
104
Voted
BMCBI
2008
125views more  BMCBI 2008»
15 years 26 days ago
XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data
Background: Advances in automated DNA sequencing technology have accelerated the generation of metagenomic DNA sequences, especially environmental ribosomal RNA gene (rDNA) sequen...
Daniel N. Frank
97
Voted
BMCBI
2007
106views more  BMCBI 2007»
15 years 26 days ago
Constructing a meaningful evolutionary average at the phylogenetic center of mass
Background: As a consequence of the evolutionary process, data collected from related species tend to be similar. This similarity by descent can obscure subtler signals in the dat...
Eric A. Stone, Arend Sidow