1 Tree of Life
Origin Notes: Part of the http://tolweb.org/tree/to characterize information about biodiversity and their evolutionary genealogy. graph features handled: Categorical nodes, Trees Graph features in papers: dynamic,dynamic (discrete) Origin Paper: Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation (https://www.notion.so/Interactive-Tree-Of-Life-iTOL-v5-an-online-tool-for-phylogenetic-tree-display-and-annotation-0b90d02cd5504ebfa21db648bc277efc?pvs=21), The Tree of Life Web Project (https://www.notion.so/The-Tree-of-Life-Web-Project-3a0dbc5490f5487e95400630b2a1df58?pvs=21) Originally found at: https://www.kaggle.com/datasets/konivat/tree-of-life?resource=download Size: 35,960 nodes, 35,959 edges Number of Graphs: 1 Appeared in years: 2023 Type of Collection: Single Graph is it stored properly?: No must be analyzed: No In repo?: Yes cleaned format?: Yes duplicate?: No link works?: Yes Added in paper: No OSF link json: https://files.osf.io/v1/resources/j7ucv/providers/osfstorage/64d90e404cf7480eec0555fd Origin paper plaintext: Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation, The Tree of Life Web Project Page id: cb0493d6b6da4a73a979f06225983011 unavailable/skip: No Cleaned ALL data: No OSF link gexf: https://files.osf.io/v1/resources/j7ucv/providers/osfstorage/64d9492294a6be103312e71d OSF link gml: https://files.osf.io/v1/resources/j7ucv/providers/osfstorage/64d96dfb4cf748115a0556b0 OSF link graphml: https://files.osf.io/v1/resources/j7ucv/providers/osfstorage/64d971350c2b4d0f65386558 first look: Yes sparkline data: {‘min’: 1, ‘max’: 416, ‘step_size’: 15, ‘num_bins’: 28, ‘bins’: [0, 15, 30, 45, 60, 75, 90, 105, 120, 135, 150, 165, 180, 195, 210, 225, 240, 255, 270, 285, 300, 315, 330, 345, 360, 375, 390, 405], ‘node_degree’: [35541, 291, 57, 35, 17, 5, 6, 0, 0, 2, 2, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1]} Related to Literature - Algorithm (Dataset tag relations) 1: Visualizing Evolving Trees (../Benchmark%20sets%200cc6b5e454304aec98f3b59b1a720476/Literature%20ad87f14e7097454fb2f784e2c8a2797a/Literature%20-%20Algorithm%2012e01bfc60a84007aa7d2d34293e123d/Visualizing%20Evolving%20Trees%203596f84acbbe46799f4f093af2f28aae.md)
2 Body
Descriptions from Literature
From “Visualizing Evolving Trees”:
The Tree of Life: captures the evolutionary progression of life on Earth [37]. The underlying data is a tree structure with a natural time component. As a new species evolves, a new node in the tree is added. The edges give the parent-child relation of the nodes, where the parent is the original species, and the child is the new species. We use a subset of this graph with 500 nodes. The maximum node degree of this tree is 5, and the radius is 24
Example Figures
From “Visualizing Evolving Trees”:
Fig. 4. Layouts obtained by the seven methods for the tree of life dataset.
== STOP RENDERING ==
From: