Difference between revisions of "Prime-phylo"

From Free Software Directory
Jump to: navigation, search
(Debian import)
 
(misc bits added)
Line 2: Line 2:
 
|Name=Prime-phylo
 
|Name=Prime-phylo
 
|Short description=bayesian estimation of gene trees taking the species tree into account
 
|Short description=bayesian estimation of gene trees taking the species tree into account
−
|Full description=PrIME (Probabilistic Integrated Models of Evolution) is a package
+
|Full description=PrIME (Probabilistic Integrated Models of Evolution) is a package supporting inference of evolutionary parameters in a Bayesian framework using Markov chain Monte Carlo simulation. A distinguishing feature of PrIME is that the species tree is taken into account when analyzing gene trees.
−
supporting inference of evolutionary parameters in a Bayesian
 
−
framework using Markov chain Monte Carlo simulation. A
 
−
distinguishing feature of PrIME is that the species tree is taken
 
−
into account when analyzing gene trees.
 
  
−
The input data to PrIME is a multiple sequence alignment in FASTA
+
The input data to PrIME is a multiple sequence alignment in FASTA format and the output data contains trees in Newick format.
−
format and the output data contains trees in Newick format.
 
 
|Homepage URL=http://prime.sbc.su.se
 
|Homepage URL=http://prime.sbc.su.se
−
|User level=
 
−
|Component programs=
 
−
|VCS checkout command=
 
−
|Computer languages=
 
−
|Status=
 
−
|Is GNU=No
 
 
|Version identifier=1.0.11-2
 
|Version identifier=1.0.11-2
−
|Version download=http://ftp.debian.org/debian/pool/main/p/prime-phylo/prime-phylo_1.0.11.orig.tar.gz  
+
|Version download=http://ftp.debian.org/debian/pool/main/p/prime-phylo/prime-phylo_1.0.11.orig.tar.gz
 
|Submitted by=Debian import
 
|Submitted by=Debian import
 
|Submitted date=2015-07-17
 
|Submitted date=2015-07-17
−
}}
+
|Status=
−
{{Import
+
|Is GNU=No
−
|Source=Debian
 
−
|Source link=http://packages.debian.org/sid/prime-phylo
 
−
|Source packages=prime-phylo 1.0.11-2
 
−
|Date=2015-07-17
 
 
}}
 
}}
 
{{Project license
 
{{Project license
 
|License=GPLv3
 
|License=GPLv3
−
|License copyright=Copyright 2002-2012 Lars Arvestad<arve@csc.kth.se>,Copyright Bengt Sennblad<bengt.sennblad@ki.se>,Copyright Jens Lagergren,Copyright Peter Andersson,Copyright Mattias FranbergCopyright Erik SjolundCopyright Joel Sjostrand,Copyright Ann-Charlotte Sonnhammer,Copyright Ikram Ullah,Copyright Orjan Akerborg
+
|License copyright=Copyright 2002-2012 Lars Arvestad <arve@csc.kth.se>, Copyright Bengt Sennblad <bengt.sennblad@ki.se>, Copyright Jens Lagergren, Copyright Peter Andersson, Copyright Mattias Franberg, Copyright Erik Sjolund, Copyright Joel Sjostrand, Copyright Ann-Charlotte Sonnhammer, Copyright Ikram Ullah, Copyright Orjan Akerborg
 
|License verified by=Debian: Andreas Tille <tille@debian.org>
 
|License verified by=Debian: Andreas Tille <tille@debian.org>
 
|License verified date=2014-10-17
 
|License verified date=2014-10-17
Line 37: Line 22:
 
{{Project license
 
{{Project license
 
|License=BSD_3Clause
 
|License=BSD_3Clause
−
|License copyright=Copyright 1997 - 2002 Takuji Nishimura, Makoto MatsumotoCopyright 2003 - 2012 Lars Arvestad<arve@csc.kth.se>,Copyright Bengt Sennblad<bengt.sennblad@ki.se>,Copyright Mattias Franberg
+
|License copyright=Copyright 1997 - 2002 Takuji Nishimura, Makoto Matsumoto. Copyright 2003 - 2012 Lars Arvestad <arve@csc.kth.se> ,Copyright Bengt Sennblad <bengt.sennblad@ki.se>, Copyright Mattias Franberg.
 
|License verified by=Debian: Andreas Tille <tille@debian.org>
 
|License verified by=Debian: Andreas Tille <tille@debian.org>
 
|License verified date=2014-10-17
 
|License verified date=2014-10-17
Line 44: Line 29:
 
{{Project license
 
{{Project license
 
|License=Other
 
|License=Other
−
|License copyright=Copyright 2001-2005 The Trustees of Indiana University. All rights reserved.Copyright 1998-2001 University of Notre Dame. All rights reservedCopyright Andrew Lumsdaine, Jeremy G. Siek, Lie-Quan LeeCopyright 2007-2012 Bengt Sennblad <bengt.sennblad@ki.se>
+
|License copyright=Copyright 2001-2005 The Trustees of Indiana University. All rights reserved.Copyright 1998-2001 University of Notre Dame. All rights reserved. Copyright Andrew Lumsdaine, Jeremy G. Siek, Lie-Quan Lee. Copyright 2007-2012 Bengt Sennblad <bengt.sennblad@ki.se>
 
|License verified by=Debian: Andreas Tille <tille@debian.org>
 
|License verified by=Debian: Andreas Tille <tille@debian.org>
 
|License verified date=2014-10-17
 
|License verified date=2014-10-17
Line 53: Line 38:
 
|Role=contact
 
|Role=contact
 
|Email=erik.sjolund@gmail.com
 
|Email=erik.sjolund@gmail.com
 +
|Resource URL=
 
}}
 
}}
 
{{Resource
 
{{Resource
 
|Resource kind=Download
 
|Resource kind=Download
 
|Resource URL=http://prime.sbc.su.se/download/
 
|Resource URL=http://prime.sbc.su.se/download/
 +
}}
 +
{{Software category
 +
|Biology=genetics
 +
|Runs-on=GNU/Linux
 +
}}
 +
{{Featured}}
 +
{{Import
 +
|Date=2015-07-17
 +
|Source=Debian
 +
|Source link=http://packages.debian.org/sid/prime-phylo
 
}}
 
}}

Revision as of 05:17, 9 September 2015


[edit]

Prime-phylo

http://prime.sbc.su.se
bayesian estimation of gene trees taking the species tree into account

PrIME (Probabilistic Integrated Models of Evolution) is a package supporting inference of evolutionary parameters in a Bayesian framework using Markov chain Monte Carlo simulation. A distinguishing feature of PrIME is that the species tree is taken into account when analyzing gene trees.

The input data to PrIME is a multiple sequence alignment in FASTA format and the output data contains trees in Newick format.



Download

http://ftp.debian.org/debian/pool/main/p/prime-phylo/prime-phylo_1.0.11.orig.tar.gz




Categories





Licensing

License

Verified by

Verified on

Notes

License

BSD 3Clause

Verified by

Debian: Andreas Tille <tille@debian.org>

Verified on

17 October 2014

Notes

License: bsd-3-clause

License

GPLv3

Verified by

Debian: Andreas Tille <tille@debian.org>

Verified on

17 October 2014

Notes

License: gpl-3

License

Other

Verified by

Debian: Andreas Tille <tille@debian.org>

Verified on

17 October 2014

Notes

License: mtl




Leaders and contributors

Contact(s)Role
Erik Sjolund contact


Resources and communication

AudienceResource typeURI
Downloadhttp://prime.sbc.su.se/download/
Debian (Ref)https://tracker.debian.org/pkg/prime-phylo


Software prerequisites




Entry














"contact" is not in the list (Maintainer, Contributor, Developer, Sponsor, Unknown) of allowed values for the "Role" property.







Date 2015-07-17
Source Debian
Source link http://packages.debian.org/sid/prime-phylo

[[Category:]]


Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the page “GNU Free Documentation License”.

The copyright and license notices on this page only apply to the text on this page. Any software or copyright-licenses or other similar notices described in this text has its own copyright notice and license, which can usually be found in the distribution or license text itself.

Retrieved from "https://directory.fsf.org/wiki?title=Prime-phylo&oldid=32910"