How to construct phylogenetic tree using MEGA 6?
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| Papers (10) | Insight |
|---|---|
179 Citations | An ideal genome tree method should be capable of using all gene families, including those containing paralogs, in a phylogenomics framework capitalizing on existing methods in conventional phylogenetic reconstruction. |
| It is therefore preferable to use parsimony-based methods as long as the number of sequences is relatively large and the branch lengths of the phylogenetic tree are relatively small. | |
11 Nov 2006 | Our results show that PBPI identifies equivalent tree estimates 1424 times faster on 256 processors than a widely-used, best-available (albeit sequential), Bayesian phylogenetic inference program. |
| I present a series of novel algorithms suitable for score-based phylogenetic tree reconstruction that demonstrably improve the accuracy of tree estimates while maintaining high computational speeds. | |
144 Citations | We suggest using k-mer distance for fast, approximate phylogenetic tree construction, and show that a speed improvement of more than three orders of magnitude can be achieved relative to standard distance methods, which require alignments. |
| Due to advances in large-scale phylogenetic inference, we argue that tree-based clustering is under-utilized. | |
| The method can hope fully will aid the reader to construct the phylogenetic tree. | |
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. |
03 Oct 2005 | We propose a new format for storing phylogenetic trees that significantly reduces storage requirements while continuing to allow the trees to be used as input to post-tree analysis. |
| Our approach also provides a new view on tree-based binary phylogenetic networks. |
Related Questions
How do scientists construct and interpret phylogenetic trees?4 answersScientists construct phylogenetic trees by utilizing various methods like UPGMA, neighbor joining, maximum likelihood, and hierarchical clustering based on genetic or physical features of organisms or biomolecules. These trees depict evolutionary relationships among species, genes, or individuals, encoding valuable information for fields like taxonomy, epidemiology, and protein classification. To interpret these trees accurately, researchers need to assess the confidence of the phylogenetic tree, often employing methods like bootstrapping, jackknifing, and statistical tests like Kishino-Hasegawa and Shimodaira-Hasegawa. Misinterpretation or misuse of phylogenetic trees can lead to misleading conclusions or misrepresentations of evolutionary theory. Therefore, understanding the construction methods and proper interpretation of phylogenetic trees is crucial in elucidating evolutionary patterns and relationships among organisms.
How to construct phylogeny trees with DNA sequences using MEGA?4 answersBuilding phylogeny trees with DNA sequences using MEGA involves several steps. First, data needs to be collected from GenBank and inserted into a text editor. Then, the data can be imported into MEGA, which is a user-friendly software for building evolutionary trees. MEGA offers different methods for constructing phylogenetic trees, such as neighbor joining and maximum likelihood. The software also provides options for aligning the sequences using algorithms like ClustalW and MUSCLE. Additionally, MEGA allows users to select the most suitable substitution model for the maximum likelihood method. Finally, MEGA provides a flexible interface for drawing the final tree for publication. By following these steps, users can construct phylogeny trees using DNA sequences in MEGA.
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