Bug#595958: ITP: paml -- Phylogenetic Analysis by Maximum Likelihood
Hello, On 09/08/2010 01:33 PM, Jeremiah Foster wrote: On Sep 7, 2010, at 17:54, Steffen Moeller wrote: * Package name: paml * URL : http://abacus.gene.ucl.ac.uk/software/paml.html * License : academics only Description : Phylogenetic Analysis by Maximum Likelihood [...] My reading of the dsfg would be that this academics only license would not be acceptable in Debian. this is correct. The paml package goes to non-free, just like e.g. clustalw. We certainly hope that after some while upstream will change that license to something that is free for everyone, but for the moment this is not the case. Steffen -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4c8d45da.9030...@gmx.de
Bug#595958: ITP: paml -- Phylogenetic Analysis by Maximum Likelihood
Hi Andreas, On 09/08/2010 08:04 AM, Andreas Tille wrote: thanks for the ITP. As you can see at http://debian-med.alioth.debian.org/tasks/bio#paml this package is also provided by BioLinux people and I'd regard this as a really cool first step to integration if you would involve the maintainer inside BioLinux in the official Debian packaging. I'd imagine that he and you are mentioned as Uploaders in a Debian Med group maintained package and you work as sponsor of him. I have looked for their package but could not find it. The only reference I saw is of version 4.4, and we aimed a 4.4c, so it could not be used directly anyway. I just met Pjotr at a meeting near Groningen. We did not have too much time and we wanted to get this done quickly. Pjotr uses PAML actively for his research and as such renders an excellent maintainer. We will find other opportunities to collaborate more with BioLinux I then thought, and our repository is open to them anyway, for them to improve whatever they feel to have done a better job with. Stuart, Oliver, Tim, I apologise should this effort have caused any inconvenience for you. The packaging resides at svn://svn.debian.org/svn/debian-med/trunk/packages/paml and Tim may already have commit rights - I don't recall if he was among those who I clicked through it when we met in Boston. Many greetings Steffen -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4c8bf412.3000...@gmx.de
Bug#595958: ITP: paml -- Phylogenetic Analysis by Maximum Likelihood
Hi Steffen, thanks for the ITP. As you can see at http://debian-med.alioth.debian.org/tasks/bio#paml this package is also provided by BioLinux people and I'd regard this as a really cool first step to integration if you would involve the maintainer inside BioLinux in the official Debian packaging. I'd imagine that he and you are mentioned as Uploaders in a Debian Med group maintained package and you work as sponsor of him. Kind regards Andreas. On Tue, Sep 07, 2010 at 05:54:13PM +0200, Steffen Moeller wrote: Package: wnpp Severity: wishlist Owner: Steffen Moeller steffen_moel...@gmx.de * Package name: paml * URL : http://abacus.gene.ucl.ac.uk/software/paml.html * License : academics only Description : Phylogenetic Analysis by Maximum Likelihood PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100908060411.gb8...@an3as.eu
Bug#595958: ITP: paml -- Phylogenetic Analysis by Maximum Likelihood
On Sep 7, 2010, at 17:54, Steffen Moeller wrote: Package: wnpp Severity: wishlist Owner: Steffen Moeller steffen_moel...@gmx.de * Package name: paml * URL : http://abacus.gene.ucl.ac.uk/software/paml.html * License : academics only Description : Phylogenetic Analysis by Maximum Likelihood PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc. Could you explain a little more about the license? It doesn't sound like it really meets the Debian Free Software Guidlines, which say; No Discrimination Against Fields of Endeavor The license must not restrict anyone from making use of the program in a specific field of endeavor. For example, it may not restrict the program from being used in a business, or from being used for genetic research. My reading of the dsfg would be that this academics only license would not be acceptable in Debian. Regards, Jeremiah -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4bb691c3-d6a7-4fa3-8c9a-72624683c...@jeremiahfoster.com
Bug#595958: ITP: paml -- Phylogenetic Analysis by Maximum Likelihood
Package: wnpp Severity: wishlist Owner: Steffen Moeller steffen_moel...@gmx.de * Package name: paml * URL : http://abacus.gene.ucl.ac.uk/software/paml.html * License : academics only Description : Phylogenetic Analysis by Maximum Likelihood PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100907155413.9324.91805.report...@toshiba.siemens
