Bug#857874: marked as done (ITP: mptp -- single-locus species delimitation)
Your message dated Wed, 22 Mar 2017 09:00:12 +0000
with message-id <E1cqc7o-00035j-8f@fasolo.debian.org>
and subject line Bug#857874: fixed in mptp 0.2.2-1
has caused the Debian Bug report #857874,
regarding ITP: mptp -- single-locus species delimitation
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.
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857874: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=857874
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--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille@debian.org>
* Package name : mptp
Version : 0.2.2
Upstream Author : Paschalia Kapli, a.o.
* URL : https://github.com/Pas-Kapli/mptp
* License : Affero
Programming Lang: C
Description : single-locus species delimitation
Implementation of a fast species delimitation method, based on PTP
(Zhang et al. 2013) with a 64-bit multi-threaded design that handles
very large datasets.
.
The tool mPTP can handle very large biodiversity datasets. It implements
a fast method to compute the ML delimitation from an inferred
phylogenetic tree of the samples. Using MCMC, it also computes the
support values for each clade, which can be used to assess the
confidence of the ML delimitation.
.
ML delimitation mPTP implements two flavours of the point-estimate
solution. First, it implements the original method from (Zhang et al.
2013) where all within-species processes are modelled with a single
exponential distribution. mPTP uses a dynamic programming implementation
which estimates the ML delimitation faster and more accurately than the
original PTP. The dynamic programming implementation has similar
properties as (Gulek et al. 2010). See the wiki for more information.
The second method assumes a distinct exponential distribution for the
branching events of each of the delimited species allowing it to fit to
a wider range of empirical datasets.
.
MCMC method mPTP generates support values for each clades. They
represent the ratio of the number of samples for which a particular node
was in the between-species process, to the total number of samples.
Remark: This package will be maintained by the Debian Med team at
https://anonscm.debian.org/git/debian-med/mptp.git
--- End Message ---
--- Begin Message ---
Source: mptp
Source-Version: 0.2.2-1
We believe that the bug you reported is fixed in the latest version of
mptp, 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 857874@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated mptp 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: SHA512
Format: 1.8
Date: Thu, 16 Mar 2017 15:21:48 +0100
Source: mptp
Binary: mptp
Architecture: source amd64
Version: 0.2.2-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
mptp - single-locus species delimitation
Closes: 857874
Changes:
mptp (0.2.2-1) unstable; urgency=medium
.
* Initial release (Closes: #857874)
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