Which software is used for phylogenetic tree?
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| Papers (16) | Insight |
|---|---|
| As an r‐package, “TreeSimGM” allows flexible and powerful stochastic phylogenetic tree simulations. | |
| Due to advances in large-scale phylogenetic inference, we argue that tree-based clustering is under-utilized. | |
| libcov can be used to compute likelihoods, search tree topologies, estimate site rates, cluster sequences, manipulate tree structures and compare phylogenies for a broad selection of applications. Using this library, it is possible to rapidly prototype applications that use the sophistication of phylogenetic likelihoods without getting involved in a major software engineering project. | |
| The software can be successfully used for population genetics, phylogenetics, taxonomic studies and other applications which require gel image analysis. | |
01 Jul 2002 139 Citations | The tree kernel can be used by any kernel-based analysis method for classification or data mining of phylogenetic profiles. |
| Representative OTUs are retained for more rigorous re-analysis. TreeTrimmer reduces the OTU density of phylogenetic trees without sacrificing taxonomic diversity while retaining the original tree topology, thereby speeding up downstream computer-intensive analyses, e. g., Bayesian and maximum likelihood tree reconstructions, in a reproducible fashion. | |
| Finally, we report that our approach is orders of magnitude more computationally efficient than full tree-based methods. We have developed an improved method for analyzing phylogenetic profiles. | |
| It is fast and versatile, has a graphic output, and can be used along with methods for phylogenetic inference on multiple alignments like PLL and Seaview. | |
| The algorithms in this paper, and the associated freely-available software, will help biologists better use and understand taxonomically labeled phylogenetic trees. | |
70 Citations | This algorithm can be used to construct phylogenetic trees from DNA sequences. |
19 Citations | Furthermore, the resulting implementation outperforms an equivalent desktop-based software implementation (using phylogenetic analysis using parsimony software) by several orders of magnitude. |
| TreeZip is an efficient approach for compressing large collections of phylogenetic trees. | |
| However any workflow that relies on phylogenetic tree analysis, could be automated with PhyloPattern. | |
28 May 2006 | Our results therefore describe the first practical phylogenetic tree reconstruction algorithm that finds guaranteed optimal solutions while being easily implemented and computationally feasible for data sets of biologically meaningful size and complexity. |
59 Citations | The new approach is a valuable alternative to existing treeevaluating methods, because it integrates phylogenetic information from the ML tree with that of trees that do not differ significantly from the ML tree. |
| These algorithms are also easily incorporated into gene tree parsimony phylogenetic analyses, potentially producing more credible estimates of reconciliation cost. |
Related Questions
How to create morphological phylogenetic tree using tools?4 answersTo create a morphological phylogenetic tree using tools, a reliable initial phylogenetic seed tree can be created using biologists' prior knowledge or existing tools such as MrBayes. Then, a top-down data processing approach can be used to construct concept-sample templates at each node in the initial phylogenetic seed tree, turning each node into a decision point with multiple concept-sample templates. A novel matching algorithm can be applied to evaluate the similarity between species' attributes and their concept-sample templates, determining the location of the species in the initial phylogenetic seed tree. This process can be repeated step by step to establish the phylogenetic tree.
How to read phylogenetic tree?5 answersReading a phylogenetic tree involves understanding a few key concepts. First, familiarize yourself with the terms autapomorphy, synapomorphy, and plesiomorphy, as these are the main new words to learn. Next, recognize that phylogenetic trees are typically presented with species-poor taxa on the left and more diverse sister taxa on the right, but this does not imply a ladder of progress from left to right. To interpret a tree, consider the branching patterns, which represent genealogical relationships among species. Look for common ancestors and monophyletic groups, which include all descendants of a common ancestor. Avoid the misconception of assuming that species on the right are more advanced or derived than those on the left. Understanding these concepts will help in correctly interpreting phylogenetic trees and avoiding common misconceptions.
What information does a phylogenetic tree provide?5 answersA phylogenetic tree provides information about the evolutionary relationships among species or groups of organisms. It shows the branching patterns, or tree topology, which represents the hypothesized evolutionary history of the taxa. Additionally, phylogenetic trees contain information about the evolutionary distances, or branch lengths, between the taxa in the tree. These branch lengths represent the amount of genetic or evolutionary change that has occurred along each branch. The tree can also provide insights into patterns of ancestry among sets of individuals and can be used to analyze and compare different phylogenies. Phylogenetic trees are important for understanding the major transitions in evolution, inferring the origin of new genes, detecting molecular adaptation, and reconstructing demographic changes in recently diverged species.
Why use phylogenetics in protein function?3 answersPhylogenetics is used in protein function prediction because it allows for the detection of conserved residues that are functionally critical. By analyzing the evolutionary relationships between proteins, phylogenetic analysis can identify functional sites that are more conserved than the rest of the protein surface. This approach is based on the principle that proteins with similar functions tend to have similar evolutionary histories. Additionally, phylogenetic profiles can be used to infer functional relationships among proteins by comparing their presence or absence across different species. By integrating information from evolutionary studies and structural analysis, phylogenetic and structural analyses can improve the accuracy of protein function inference. Furthermore, phylogenomic analysis, which combines phylogenetic tree construction with experimental data integration, can provide insights into protein superfamily evolution and improve functional classification.
How do you construct a phylogenetic tree using NCBI?3 answers
What software is used for phylogenetic tree?6 answers