123views more  BMCBI 2004»
13 years 6 months ago
galaxieEST: addressing EST identity through automated phylogenetic analysis
Background: Research involving expressed sequence tags (ESTs) is intricately coupled to the existence of large, well-annotated sequence repositories. Comparatively complete and sa...
R. Henrik Nilsson, Balaji Rajashekar, Karl-Henrik ...
76views more  APPML 2002»
13 years 6 months ago
Proper gromov transforms of metrics are metrics
In phylogenetic analysis, a standard problem is to approximate a given metric by an additive metric. Here it is shown that, given a metric D defined on some finite set X and a non...
Andreas W. M. Dress
101views more  TCBB 2008»
13 years 6 months ago
Improved Layout of Phylogenetic Networks
Split networks are increasingly being used in phylogenetic analysis. Usually, a simple equal-angle algorithm is used to draw such networks, producing layouts that leave much room f...
Philippe Gambette, Daniel H. Huson
92views more  IJBRA 2006»
13 years 6 months ago
Jumpstarting phylogenetic analysis
: Phylogenetic analysis is a central tool in studies of comparative genomics. When a new region of DNA is isolated and sequenced, researchers are often forced to throw away months ...
Jesse Mecham, Mark J. Clement, Quinn Snell, Todd F...
116views more  BMCBI 2006»
13 years 6 months ago
TaxMan: a taxonomic database manager
Background: Phylogenetic analysis of large, multiple-gene datasets, assembled from public sequence databases, is rapidly becoming a popular way to approach difficult phylogenetic ...
Martin Jones, Mark Blaxter
163views more  ALGORITHMICA 2006»
13 years 6 months ago
Building Large Phylogenetic Trees on Coarse-Grained Parallel Machines
Phylogenetic analysis is an area of computational biology concerned with the reconstruction of evolutionary relationships between organisms, genes, and gene families. Maximum likel...
Thomas M. Keane, Andrew J. Page, Thomas J. Naughto...
155views more  ALMOB 2007»
13 years 6 months ago
Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid rep
Background: Some amino acid residues functionally interact with each other. This interaction will result in an evolutionary co-variation between these residues – coevolution. Ou...
Rodrigo Gouveia-Oliveira, Anders Gorm Pedersen
136views Bioinformatics» more  CSB 2005»
13 years 12 months ago
Whole Genome Phylogeny Based on Clustered Signature String Composition
Peptide compositions constructed out of whole sets of protein sequences can be used as species signatures for phylogenetic analysis. To account for point mutations, an amino acid ...
Xiaomeng Wu, Guohui Lin, Xiu-Feng Wan, Dong Xu