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Compare2Trees
An algorithm and software tool for comparing alternative phylogenetic trees. The main application of the software is to compare phylogenies obtained using different phylogenetic methods for some fixed set of species or obtained using different gene sequences from those species. The algorithm pairs up each branch in one phylogeny with a matching branch in the second phylogeny and finds the optimum 1-to-1 map between branches in the two trees in terms of a topological score.
TreeVersity
A web based interactive data visualization tool that allows users to analyze change in datasets by creating dynamic hierarchies based on the data attributes. TreeVersity2 introduces a novel space filling visualization (StemView) to represent change in trees at multiple levels--not just at the leaf level. With this visualization users can explore absolute and relative changes, created and removed nodes, and each node's actual values, while maintaining the context of the tree. In addition, TreeVersity2 provides overviews of change over the entire time period, and a reporting tool that lists outliers in textual form, which helps users identify the major changes in the data without having to manually setup filters.
BeeTLe / Better Treelength
Analyzes a large number of simulated and biological datasets. BeeTLe is a simple heuristic that runs a collection of methods, including POY, a method which seeks a tree/alignment pair minimizing the total treelength. It produces a set of trees on a given input set of unaligned sequences, uses POY to compute the treelength of each tree, and then returns the tree that had the shortest treelength. It is guaranteed to find trees at least as short as those found using POY, and thus enables to evaluate the impact of using treelength to find trees.
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