[Biojava-dev] SNP analyses in Biojava2

[Michael Heuer]

On Fri, 14 May 2004, Bruno Aranda - eBioIntel wrote:

> We are endeavouring a project about SNP and related stuff and, of course,
> it will be using BioJava. It is a long term project and we are now in
> early design. What I would like it to do is to analyze the SNPs with
> summary statistics,  neutrality tests, coalescent and other things. As we
> are just in the earliest thoughts and it will be using J2SE 1.5 I think
> that all this SNP api would be a good contribution to Biojava 2. So, is
> there any specification about, for instance, how to do statistical
> equation classes in Biojava 2 (just the classes with the equations to
> process statistics)... it is too early for this? Of course I can do it
> aside BioJava but, if I make all these classes with the bjv2 phylosophy,
> then it will be easier to include them...

Take a look at the COLT library

> http://dsd.lbl.gov/~hoschek/colt/

the commons-math library

> http://jakarta.apache.org/commons/math

or perhaps making calls out to the R statistical package

> http://www.r-project.org

I don't think the biojava or bjv2 library is the right place for the
statistics classes.  SNP api on the other hand ...

    michael