Hi Shakuntala, The method for global alignment in BioJava is Needleman Wunsch.
http://www.biojava.org/docs/api/org/biojava3/alignment/NeedlemanWunsch.html Andreas On Fri, Apr 18, 2014 at 3:08 AM, Shakuntala Baichoo <shak...@uom.ac.mu>wrote: > Hi! > Can anyone tell me which method is used by Alignments.getAllPairsScorers to > find the pairwise distance for global alignments? Is it the method > described by Kimura et al? > > Thanks. > > Shakuntala > > > > On Tue, Apr 15, 2014 at 8:00 PM, <biojava-l-requ...@lists.open-bio.org > >wrote: > > > Send Biojava-l mailing list submissions to > > biojava-l@lists.open-bio.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > or, via email, send a message with subject or body 'help' to > > biojava-l-requ...@lists.open-bio.org > > > > You can reach the person managing the list at > > biojava-l-ow...@lists.open-bio.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Biojava-l digest..." > > > > > > Today's Topics: > > > > 1. doubt about version... (Kelvin Vieira Kredens) > > 2. Re: doubt about version... (Andreas Prlic) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 14 Apr 2014 16:11:49 -0300 > > From: Kelvin Vieira Kredens <kred...@gmail.com> > > Subject: [Biojava-l] doubt about version... > > To: biojava-l@lists.open-bio.org > > Message-ID: > > <CACU5nmcdA+cRqXMDoSmgzu+eBkJSxuk= > > zqthzahpherrnb-...@mail.gmail.com> > > Content-Type: text/plain; charset=UTF-8 > > > > Hi, I'm a brazilian doctoral student in computer sciences.... I'm in the > > very beginning of my studies... > > > > I will work with DNA datasets... with some data mining questions... > > > > I found this API BioJava and I want to use it... But I've a doubt about > > what version I should use. > > > > the version 3 is new, but have little information about... and version 1 > is > > older but I found lots of information... > > > > I'm thinking about use version 1... what will be the greatest problems I > > will need to deal about this choice? > > > > Is there any source of information about version 3? > > > > -- > > Atenciosamente, > > > > Kelvin Vieira Kredens > > ?N?o seria ci?ncia se tivesse garantias, e, francamente, seria um pouco > > chato. Mas n?o buscar?amos algo se fosse uma causa perdida? - Rick > > Gaitskell (f?sico procurando evid?ncias de mat?ria escura) > > > > > > > > ------------------------------ > > > > Message: 2 > > Date: Mon, 14 Apr 2014 13:59:41 -0700 > > From: Andreas Prlic <andr...@sdsc.edu> > > Subject: Re: [Biojava-l] doubt about version... > > To: Kelvin Vieira Kredens <kred...@gmail.com> > > Cc: Biojava <biojava-l@lists.open-bio.org> > > Message-ID: > > < > > calthepx81hnvpiwpn3pbs7odsbxaqdryv0ogxkaj2xyqj69...@mail.gmail.com> > > Content-Type: text/plain; charset=UTF-8 > > > > Hi Kelvin, > > > > It depends what specific features you want. > > > > Take a look at the cookbook > > > > http://biojava.org/wiki/BioJava:CookBook > > > > and also the javadoc... > > > > http://www.biojava.org/docs/api/index.html > > > > Andreas > > > > > > On Mon, Apr 14, 2014 at 12:11 PM, Kelvin Vieira Kredens > > <kred...@gmail.com>wrote: > > > > > Hi, I'm a brazilian doctoral student in computer sciences.... I'm in > the > > > very beginning of my studies... > > > > > > I will work with DNA datasets... with some data mining questions... > > > > > > I found this API BioJava and I want to use it... But I've a doubt about > > > what version I should use. > > > > > > the version 3 is new, but have little information about... and version > 1 > > is > > > older but I found lots of information... > > > > > > I'm thinking about use version 1... what will be the greatest problems > I > > > will need to deal about this choice? > > > > > > Is there any source of information about version 3? > > > > > > -- > > > Atenciosamente, > > > > > > Kelvin Vieira Kredens > > > ?N?o seria ci?ncia se tivesse garantias, e, francamente, seria um pouco > > > chato. Mas n?o buscar?amos algo se fosse uma causa perdida? - Rick > > > Gaitskell (f?sico procurando evid?ncias de mat?ria escura) > > > > > > _______________________________________________ > > > Biojava-l mailing list - Biojava-l@lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > > > > ------------------------------ > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l@lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > End of Biojava-l Digest, Vol 134, Issue 2 > > ***************************************** > > > > -- > > Email Disclaimer: This email and all its contents are subject to the > disclaimer at http://www.uom.ac.mu/emaildisclaimer > > -- > <http://www.uom.ac.mu> > _______________________________________________ > Biojava-l mailing list - Biojava-l@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - Biojava-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l
