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AutoFACT: An Automatic Functional Annotation and Classification Tool
(2005)
BACKGROUND:Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process ...
SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics
(2007)
BACKGROUND:Phylogenetic analyses based on datasets rich in both genes and species (phylogenomics) are becoming a standard approach to resolve evolutionary questions. However, several difficulties are associated with the ...
iVici: Interrelational Visualization and Correlation Interface
(2005)
We have developed an application, iVici, to analyze cellular networks represented as addressable symmetric or asymmetric two-dimensional matrices. iVici was designed to permit simultaneous visualization and correlation of ...
A maximum likelihood framework for protein design
(2006)
BACKGROUND:The aim of protein design is to predict amino-acid sequences compatible with a given target structure. Traditionally envisioned as a purely thermodynamic question, this problem can also be understood in a wider ...
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
(2007)
BACKGROUND:Thanks to the large amount of signal contained in genome-wide sequence alignments, phylogenomic analyses are converging towards highly supported trees. However, high statistical support does not imply that the ...
AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis
(2003)
BACKGROUND:Sequence data analyses such as gene identification, structure modeling or phylogenetic tree inference involve a variety of bioinformatics software tools. Due to the heterogeneity of bioinformatics tools in usage ...
Heterotachy and long-branch attraction in phylogenetics
(2005)
BACKGROUND:Probabilistic methods have progressively supplanted the Maximum Parsimony (MP) method for inferring phylogenetic trees. One of the major reasons for this shift was that MP is much more sensitive to the Long ...
Three rounds (1R/2R/3R) of genome duplications and the evolution of the glycolytic pathway in vertebrates
(2006)
BACKGROUND:Evolution of the deuterostome lineage was accompanied by an increase in systematic complexity especially with regard to highly specialized tissues and organs. Based on the observation of an increased number of ...
Bone mineral density measurement and osteoporosis treatment after a fragility fracture in older adults: regional variation and determinants of use in Quebec
(2005)
BACKGROUND:Osteoporosis (OP) is a skeletal disorder characterized by reduced bone strength and predisposition to increased risk of fracture, with consequent increased risk of morbidity and mortality. It is therefore an ...
Overview of the First Phylogenomics Conference
(2007)
The First Phylogenomics Conference was held in Ste-Adèle (Québec, Canada) in March 2006. Selected papers appear in this special issue of BMC Evolutionary Biology. Here, we give an introduction to the field and provide an ...