Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution
Hahn, M. (2007) Genome Biology.
FIGURE CAPTION
Figure 3. Mammalian species tree. A phylogenetic tree of the six species considered in the text is shown (branches are not proportional to time). Non-informative branches are marked with an arrow.
PhyloFinder: An intelligent search engine for phylogenetic tree databases
Chen, D., Burleigh, J., Bansal, M., Fernández-Baca, D. (2008) BMC Evolutionary Biology.
FIGURE CAPTION
Figure 9. Tree mining using LCA mappings.
PhyloFinder: An intelligent search engine for phylogenetic tree databases
Chen, D., Burleigh, J., Bansal, M., Fernández-Baca, D. (2008) BMC Evolutionary Biology.
FIGURE CAPTION
Figure 3. Tree mining: pruned, embedded, and refined. In this example, the query tree Q1 is a pruned subtree and an embedded subtree of tree T; Q1 is also (trivially) refined within T. The query tree Q2 is an... Show Full Caption
PhyloFinder: An intelligent search engine for phylogenetic tree databases
Chen, D., Burleigh, J., Bansal, M., Fernández-Baca, D. (2008) BMC Evolutionary Biology.
FIGURE CAPTION
Figure 5. A slight modification of nested-set representation of a rooted tree.
PhyloFinder: An intelligent search engine for phylogenetic tree databases
Chen, D., Burleigh, J., Bansal, M., Fernández-Baca, D. (2008) BMC Evolutionary Biology.
FIGURE CAPTION
Figure 2. T(A) and T|A. For A = {a, f, g}, T1 is the tree T(A) and T2 is the tree T|A.
Rooting a phylogenetic tree with nonreversible substitution models
Yap, V., Speed, T. (2005) BMC Evolutionary Biology.
FIGURE CAPTION
Figure 2. Unrooted tree for nine primate mtDNA sequences The assumed unrooted tree is that presented in Yang [5]. The branches adjacent to leaf nodes are referred to by the corresponding organisms, while the interior branches are labelled a through f as indicated.
Rooting a phylogenetic tree with nonreversible substitution models
Yap, V., Speed, T. (2005) BMC Evolutionary Biology.
FIGURE CAPTION
Figure 1. Unrooted tree with four taxa The four branches adjacent to leaf nodes will be referred to by the corresponding taxon names.
Orthology prediction at scalable resolution by phylogenetic tree analysis
van der Heijden, R., Snel, B., van Noort, V., Huynen, M. (2007) BMC Bioinformatics.
FIGURE CAPTION
Figure 1. Levels Of Orthology From Trees. Genes in a subsection of the tree for COG4565 (transcription regulatory protein Dpia) have been numbered according their levels of relatedness. The tree has been analyzed for gene duplication (red squares) and speciation events (green circles), after which... Show Full Caption
Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices
Craig, R., Liao, L. (2007) BMC Bioinformatics.
FIGURE CAPTION
Figure 3. Schematic illustration of TreeSec method to derive super phylogenetic vector from a distance matrix for a given protein from the distance matrix of its orthologous proteins A, B, ..., H. Section 1 across the tree leads to four clusters of the orthologous proteins:... Show Full Caption
Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution
Hahn, M. (2007) Genome Biology.
FIGURE CAPTION
Figure 1. Two examples of tree reconciliation. In both (a) and (b) the leftmost tree represents the gene tree, the middle tree the reconciled gene tree showing the duplications and losses, and the rightmost tree shows the species 
Universal Scaling in the Branching of the Tree of Life
Herrada, E., Tessone, C., Klemm, K., Eguíluz, V., Hernández-García, E., Duarte, C. (2008) PLoS ONE.
FIGURE CAPTION
Figure 1. Branch size and cumulative branch size examples. The values of the branch size (A) and of the cumulative branch size (C) are shown (in brackets, as (A,C)) at each node of three small example trees. A:... Show Full Caption
Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices
Craig, R., Liao, L. (2007) BMC Bioinformatics.
FIGURE CAPTION
Figure 2. Illustration of how the elements of the distance matrices correspond to distances between leaves on the phylogenetic trees. In matrix A, element (i, j) corresponds to a pair of neighboring genomes, whereas element (i', j') to a pair of genomes that are distantly positioned... Show Full Caption
Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution
Hahn, M. (2007) Genome Biology.
FIGURE CAPTION
Figure 2. Tree reconciliation bias. (a) The effect of wrongly inferring the gene tree: the addition of one duplication and three losses. (b) An example where a low bootstrap value (65%) below the cut-off results in the collapse of the gene tree. As a result, no duplications or losses are inferred.
Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution
Hahn, M. (2007) Genome Biology.
FIGURE CAPTION
Figure 6. Slight bias towards placing duplicates on the tips of the tree. (a) Shows how gains and losses would be inferred for the gene tree shown. (b) Taking into account bootstrap support can result in placing duplicates towards the tips as gene tree topologies are collapsed.
Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution
Hahn, M. (2007) Genome Biology.
FIGURE CAPTION
Figure 7. Relationship between tree reconciliation and likelihood methods for estimating the number of gene gains. The number of gene duplicates inferred on only informative branches of the (a) mammalian tree, and (b) Drosophila tree are shown.
Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment
Hartmann, S., Vision, T. (2008) BMC Evolutionary Biology.
FIGURE CAPTION
Figure 4. Overview of SIA method. 1. Initial gappy alignment (The example shows an alignment of six sequences (A-F). "X" represents any amino acid; "-" represents a gap or missing data.); 2. The overlap-graph and two maximal cliques (green and purple); 3. Assignment of columns... Show Full Caption
Rooting the eutherian tree: the power and pitfalls of phylogenomics
Nishihara, H., Okada, N., Hasegawa, M. (2007) Genome Biology.
FIGURE CAPTION
Figure 1. Three phylogenetic hypotheses for the root of theeutherian tree. (a) Tree 1: basal Afrotheria. (b) Tree 2: basal Xenarthra. (c) Tree 3: basal Boreotheria, or Afrotheria/Xenarthra clade. The phylogenetic relationships within Boreotheria (cow, dog, mouse, rat, human, chimpanzee, and macaque) are fixed in this study.
Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution
Hahn, M. (2007) Genome Biology.
FIGURE CAPTION
Figure 4. The effect of tree reconciliation bias. The graphs show the relationship between the number of gains and losses inferred as a function of the bootstrap cut-off used for (a) the mammalian tree, and (b) the Drosophila tree. The numbers represent... Show Full Caption
Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution
Hahn, M. (2007) Genome Biology.
FIGURE CAPTION
Figure 5. Accounting for tree reconciliation bias. The graphs show the relationship between the number of gains and losses inferred as a function of the bootstrap cut-off used for (a) the mammalian tree, and (b) the Drosophila tree. The numbers represent the... Show Full Caption
Tree of Life Based on Genome Context Networks
Ding, G., Yu, Z., Zhao, J., Wang, Z., Li, Y., Xing, X., Wang, C., Liu, L., Li, Y. (2008) PLoS ONE.
FIGURE CAPTION
Figure 3. Influence of accuracy and number of edges in the gene networks on tree building. The template tree was based on the consensus tree in Figure 2 in both panels.... Show Full Caption