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

Bug#1038668: marked as done (ITP: veryfasttree -- Speeding up the estimation of phylogenetic trees for large alignments through parallelization and vectorization strategies)

Your message dated Wed, 19 Jul 2023 18:10:26 +0000
with message-id <E1qMBd4-007sqS-HC@fasolo.debian.org>
and subject line Bug#1038668: fixed in veryfasttree 4.0.1+dfsg-1
has caused the Debian Bug report #1038668,
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.)


-- 
1038668: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1038668
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 --- 
Source: veryfasttree
Source-Version: 4.0.1+dfsg-1
Done: César Pomar <cesaralfredo.pineiro@usc.es>

We believe that the bug you reported is fixed in the latest version of
veryfasttree, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1038668@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
César Pomar <cesaralfredo.pineiro@usc.es> (supplier of updated veryfasttree package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Tue, 11 Jul 2023 15:53:44 +0200
Source: veryfasttree
Binary: veryfasttree veryfasttree-dbgsym
Architecture: source amd64
Version: 4.0.1+dfsg-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: César Pomar <cesaralfredo.pineiro@usc.es>
Description:
 veryfasttree - Speeding up the estimation of phylogenetic trees from sequences
Closes: 1038668
Changes:
 veryfasttree (4.0.1+dfsg-1) unstable; urgency=low
 .
   * Initial release (Closes: #1038668)
Checksums-Sha1:
 eed8414605fcd459ab7e28d0aaf2adec4802f423 2133 veryfasttree_4.0.1+dfsg-1.dsc
 3135b6136f12308e7879fad4b0707fb7106ac433 161084 veryfasttree_4.0.1+dfsg.orig.tar.xz
 6b8c2cf2b240a9a1b30e303315fde2ead9e4578b 35204 veryfasttree_4.0.1+dfsg-1.debian.tar.xz
 c291ec272d0db5318c92c24b2f7d77d482bf3830 69363676 veryfasttree-dbgsym_4.0.1+dfsg-1_amd64.deb
 4b1dd6f5eb2e34aabe6d8b1a11ed20f57e431b29 7148 veryfasttree_4.0.1+dfsg-1_amd64.buildinfo
 cbb551de8f0bf96a2a63093ab018be67df019e4a 2199568 veryfasttree_4.0.1+dfsg-1_amd64.deb
Checksums-Sha256:
 d3dc7ca910cc9769be23c840c9d882418293c61d0a7b138a232f7932a52a2291 2133 veryfasttree_4.0.1+dfsg-1.dsc
 efefae05266caef15c92eb1e266ff626f7058caca7ebeb60c5e724211ae3c6e8 161084 veryfasttree_4.0.1+dfsg.orig.tar.xz
 9d6813978d9776bd499880423343f43132bf437d04e38c62b26fe78d98ec848b 35204 veryfasttree_4.0.1+dfsg-1.debian.tar.xz
 45b631c0ed6e8eb2c0e81a68c31b154f14c3a24a9b004c1b9cd1d931b08b07a4 69363676 veryfasttree-dbgsym_4.0.1+dfsg-1_amd64.deb
 f20c882e97c356d058e96fd1ce6a3d1a9b6aff195b12c48bd151e13ffc2e6142 7148 veryfasttree_4.0.1+dfsg-1_amd64.buildinfo
 7d2422ce385585ef74f743e3a7b64429bd7dad5bf2a6c90215a57a70a42e16c2 2199568 veryfasttree_4.0.1+dfsg-1_amd64.deb
Files:
 249c6d90e6ecd45cc962d3d4dfd3e5c8 2133 science optional veryfasttree_4.0.1+dfsg-1.dsc
 9823b47fea839cd7069086b3bca342c8 161084 science optional veryfasttree_4.0.1+dfsg.orig.tar.xz
 f9b8ceb050435294f0ae599944be4601 35204 science optional veryfasttree_4.0.1+dfsg-1.debian.tar.xz
 e9e3c001047b633696ec11852fb3b321 69363676 debug optional veryfasttree-dbgsym_4.0.1+dfsg-1_amd64.deb
 4840792eb9e3cc4a46d0e69125ca1274 7148 science optional veryfasttree_4.0.1+dfsg-1_amd64.buildinfo
 f5d6dd63e6cd52dba0978254931b0c95 2199568 science optional veryfasttree_4.0.1+dfsg-1_amd64.deb

-----BEGIN PGP SIGNATURE-----
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=8B6N
-----END PGP SIGNATURE-----

--- End Message ---
Reply to: