What about: http://en.wikipedia.org/wiki/MUSCLE_(alignment_software)
It's public domain. Another Multiple Sequence Alignment would be t-coffee, but it's GPL again. Hannes On Sun, Mar 18, 2012 at 21:47, Spencer Bliven <[email protected]> wrote: > Unfortunately, HMMER is licensed as GPL. As such, we can't port it to > BioJava or even link against it with JNI. A 2009 > post<http://selab.janelia.org/people/eddys/blog/?p=127>indicates that > they are not interested in re-licensing HMMER under a less > restrictive license. I think we should move away from any HMMER-port > project, and focus on porting other important algorithms such as BLAST (public > domain<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/blast/LICENSE> > ). > > I went ahead and removed HMMER from the GSoC wiki > page<http://biojava.org/wiki/Google_Summer_of_Code_2012>. > I was trying to think of other LGPL-compatable bioinformatics > projects<http://en.wikipedia.org/wiki/List_of_open_source_bioinformatics_software>which > would be nice to port to biojava. Maybe a sequence browser, such as > incorporating/linking the Integrated Genome > Browser<http://en.wikipedia.org/wiki/Integrated_Genome_Browser>? > Anyone have ideas other than BLAST? > > -Spencer > > On Sat, Mar 17, 2012 at 02:50, Ritisha Laungani > <[email protected]>wrote: > >> Hello, >> >> I am Ritisha Laungani, a pre-final year student currently persuing *MSc >> Tech. Information Systems* at Birla Institute of Technology and Science, >> Goa, India. >> >> I would like to apply for the BioJava project as i have worked into all the >> 3 fields this projects requires- C, Java and Bio! >> >> As far as i understand, in simple terms, the project's goal is to convert >> an existing HMMER source code, which is written in C, to a java code using >> language processing tools. Do correct me if i am wrong here! >> >> I must admit here that i am new to open source software development and >> also unaware of HMMER. But i would love to learn if given a chance and the >> correct resources! :) >> >> Eagerly awaiting a reply, which could guide me to the next step. >> >> Regards, >> >> Ritisha Laungani >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
