Bug#1038668: veryfasttree_4.0.1+dfsg-1_amd64.changes REJECTED
Dear Thorsten, As the author of the tool, I can provide an answer. I started implementing VeryFastTree in April 2019, using FastTree 2.1.10 (http://www.microbesonline.org/fasttree/FastTree-2.1.10.c) as the base, which was the latest version at that time. This version was released on April 11, 2017 (http://www.microbesonline.org/fasttree/ChangeLog), although the function attributed to Stephane Guindon, according to the author, was included in version 2.1.0 on October 15, 2009. Best regards, and thanks to both of you for your work, César De: Thorsten Alteholz Enviado: martes, 11 de julio de 2023 21:00 Para: Debian Med Packaging Team ; PIÑEIRO POMAR CESAR ALFREDO ; ti...@debian.org Asunto: veryfasttree_4.0.1+dfsg-1_amd64.changes REJECTED [No suele recibir correo electrónico de ftpmas...@ftp-master.debian.org. Descubra por qué esto es importante en https://aka.ms/LearnAboutSenderIdentification ] Hi Andreas, according to [1] the code from Stephane Guindon was added 2019-05-11 whereas according to [2] the license of pyhml was already changed to GPL-3 in 2018-08-29 ... Was the code really based on an earlier version? Thorsten [1] https://github.com/citiususc/veryfasttree/blame/master/src/NeighbourJoining.tcc [2] https://github.com/stephaneguindon/phyml/commit/0893faa043c47bf5bc78c5388900fec5b7e77205 === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. ___ Debian-med-packaging mailing list debian-med-packag...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
Bug#1038669: RFS: veryfasttree/4.0-1 [ITP] -- Speeding up the estimation of phylogenetic trees from sequences
Package: sponsorship-requests Severity: wishlist Dear mentors, I am looking for a sponsor for my package "veryfasttree": * Package name : veryfasttree Version : 4.0-1 Upstream contact : César Pomar * URL : https://github.com/citiususc/veryfasttree * License : MPL-2.0, Custom-License-2, BSD-2-clause, MIT, GPL-3.0, BSL-1.0, Custom-License-3, Custom-License-1 * Vcs : https://github.com/citiususc/veryfasttree Section : science The source builds the following binary packages: veryfasttree - Speeding up the estimation of phylogenetic trees from sequences To access further information about this package, please visit the following URL: https://mentors.debian.net/package/veryfasttree/ Alternatively, you can download the package with 'dget' using this command: dget -x https://mentors.debian.net/debian/pool/main/v/veryfasttree/veryfasttree_4.0-1.dsc Changes for the initial release: veryfasttree (4.0-1) unstable; urgency=low . *Closes: #1038668 *Introduction of new thread levels for improved parallelization. *Enhanced performance through new parallel regions (e.g., ML Lengths, ML splits, LogLk, etc.). *Threads used in tree creation: Top hits, TopHitNJSearch, FastNJSearch, and ExhaustiveNJSearch(-slow). *Implementation of a faster tree partitioning approach with significant speed improvements. *Tree partitioning limited to NNI, SPR, and upProfiles computations for memory conservation. *Parallel tree traversal implemented for remaining parts. *Replacement of disk storage for profiles with Disk Computing. *Shared and reused Top upProfiles among threads for memory efficiency and accelerated sequential parts. *Improved non-deterministic mode with removal of mutex usage. *Optimized performance by parallelizing non-deterministic parts in deterministic mode. *Also implemented non-deterministic parts in deterministic mode for improved performance. *Deterministic mode now outperforms non-deterministic mode in terms of speed. *Tree partitioning method logging now hidden by default. *Support for Fastq format and libBZ2 compression. *Support for reading trees from NEXUS block trees. *Nvidia CUDA GPU computing support. (Experimental) *Introduced parallel compilation. *Incorporation of changes from FastTree-2.11. *Clang Support *Addressed critical errors and implemented substantial corrections. Regards, -- César Pomar
Bug#1038668: ITP: veryfasttree -- Speeding up the estimation of phylogenetic trees for large alignments through parallelization and vectorization strategies
Package: wnpp Severity: wishlist Owner: Cesar Pomar * Package name: veryfasttree Version : 4.0 Upstream Author : Cesar Pomar * 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.
Bug#1038643: veryfasttree -- Speeding up the estimation of phylogenetic trees for large alignments through parallelization and vectorization strategies
Package: wnpp Severity: wishlist Owner: Cesar Pomar * Package name: veryfasttree Version : 4.0 Upstream Author : Cesar Pomar * 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.
