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» Visualizations for taxonomic and phylogenetic trees
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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
BIOINFORMATICS
2008
106views more  BIOINFORMATICS 2008»
14 years 9 months ago
Interactive visualization software for exploring phylogenetic trees and clades
The Summary Tree Explorer (STE) is a Java application for interactively exploring sets of phylogenetic trees using two coupled representations: a node-and-link diagram and a textu...
Mark Derthick
BMCBI
2011
14 years 1 months ago
PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus ge
Background: Results of phylogenetic analysis are often visualized as phylogenetic trees. Such a tree can typically only include up to a few hundred sequences. When more than a few...
Jiajie Zhang, Amir Madany Mamlouk, Thomas Martinet...
ACIIDS
2010
IEEE
153views Database» more  ACIIDS 2010»
14 years 10 months ago
Visualization of Influenza Protein Segment HA in Manifold Space
Due to the lateral gene transfer, the phylogenetic tree may be inadequate for representing the evolution of Influenza A (H1N1) virus. This work employs the distance invariant manif...
Cheng-Yuan Liou, Wei-Chen Cheng
BMCBI
2010
142views more  BMCBI 2010»
14 years 9 months ago
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
Background: Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-ba...
Frederick A. Matsen III, Robin B. Kodner, E. Virgi...