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» Visualizations for taxonomic and phylogenetic trees
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BMCBI
2007
162views more  BMCBI 2007»
13 years 5 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»
13 years 5 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
12 years 9 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»
13 years 6 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»
13 years 5 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...