Package: wnpp Severity: wishlist Owner: Cesar Pomar <cesaralfredo.pine...@usc.es>
* Package name : veryfasttree Version : 4.0 Upstream Author : Cesar Pomar <cesaralfredo.pine...@usc.es> * URL : https://github.com/citiususc/veryfasttree * License : GPL Programming Lang: C++ Description : Speeding up the estimation of phylogenetic trees for large alignments through parallelization and vectorization strategies VeryFastTree is a highly efficient implementation inspired by the FastTree-2 tool, designed to expedite the inference of approximately-maximum-likelihood phylogenetic trees from nucleotide or protein sequence alignments. It is an optimized implementation designed to accelerate the estimation of phylogenies for large alignments. By leveraging parallelization and vectorization strategies, VeryFastTree significantly improves the performance and scalability of phylogenetic analysis, allowing it to construct phylogenetic trees in a fraction of the time previously required. Maintaining the integrity of FastTree-2, VeryFastTree retains the same phases, methods, and heuristics used for estimating phylogenetic trees. This ensures that the topological accuracy of the trees produced by VeryFastTree remains equivalent to that of FastTree-2. Moreover, unlike the parallel version of FastTree-2, VeryFastTree guarantees deterministic results, eliminating any potential variations in the output. To facilitate a seamless transition for users, VeryFastTree adopts the exact same command line arguments as FastTree-2. This means that by simply substituting FastTree-2 with VeryFastTree, and using the same set of options, users can significantly enhance the overall performance of their phylogenetic analyses. - why is veryfasttree useful/relevant? if there are other packages providing similar functionality, how does it compare?: VeryFastTree is a highly tuned implementation of the FastTree(which is already published in the Debian repositories). VeryFastTree takes advantage of parallelization and vectorization strategies to boost performance. In our publication[1], we demonstrated that VeryFastTree performs between 7.8x and 3.5x times faster than FastTree for the same input and options. We are currently working on a second publication with version 4.0, where we show an even greater performance improvement, we can complete the creation of phylogenetic trees with 2 million sequences in just a couple of days, whereas it would take FastTree more than two weeks. [1] VeryFastTree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies, César Piñeiro, José M. Abuín, and Juan C. Pichel, Bioinformatics, vol. 36, no. 17, pages 4658-4659, 2020. -how do you plan to maintain it?. do you need a sponsor?: Until now, the tool has been maintained through GitHub issues. As the authors of the tool, we will resolve the problems that are reported. Yes, we are looking for a sponsor for the publication of the package.
