[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Bug#1038643: marked as done (ITP: veryfasttree -- speeding up the estimation of phylogenetic trees for large alignments through parallelization and vectorization strategies)

Your message dated Mon, 21 Aug 2023 16:55:06 +0200
with message-id <ZON6yl7YWW2OkRkx@fusion>
and subject line ITP: veryfasttree: closing duplicate
has caused the Debian Bug report #1038643,
regarding ITP: veryfasttree -- speeding up the estimation of phylogenetic trees for large alignments through parallelization and vectorization strategies
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact owner@bugs.debian.org
immediately.)


-- 
1038643: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1038643
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Cesar Pomar <cesaralfredo.pineiro@usc.es>

* Package name    : veryfasttree
  Version         : 4.0
  Upstream Author : Cesar Pomar <cesaralfredo.pineiro@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.

--- End Message ---
--- Begin Message --- 
Package: veryfasttree
Version: 4.0.1+dfsg-1

This was a duplicate entry of #1038668.

Have a nice day,  :)
-- 
  .''`.  Étienne Mollier <emollier@debian.org>
 : :' :  gpg: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
 `. `'   sent from /dev/pts/5, please excuse my verbosity
   `-    on air: Royal Hunt - Thorn In My Heart

Attachment: signature.asc
Description: PGP signature


--- End Message ---
Reply to: