Hi Steven,

I'm a bit hazy on population genetics myself - I was using Bioconductor
packages for analysis of gene expression experiments done on microarrays and
/ or real time PCR.

However, Bioconductor has an extremely helpful and active mailing list, and
I do seem to remember some discussion on it a while ago regarding a package
dealing with a similar situation to yours.  In the first instance, you could
browse through the brief descriptions of the packages:

http://www.bioconductor.org/packages/2.6/bioc/

where you will find a number that are made to analyze sequences, for example
GeneR, GeneRfold, GeneticsPed, cosmo etc.  Click on the name of the package
to see a more detailed description, you can also look at the help files /
manuals / vignettes for each package from there.

If you are still not sure if there is anything that fits your needs, you
could also email the bioconductor mailing group:

http://www.bioconductor.org/docs/mailList.html

Hope it helps,
Best
Amy



On Tue, May 25, 2010 at 7:23 PM, Steven Lembark <lembark@wrkhors.com> wrote:

> On Tue, 25 May 2010 16:46:17 +0100
> Amy Mikhail <amy.mikhail@googlemail.com> wrote:
>
> > Dear Steven,
> >
> > There are lots of factor analysis packages in R,  but it sounds from the
> > below like you want something that can handle sequences too.  Have you
> tried
> > looking in Bioconductor:
> >
> > http://www.bioconductor.org/
>
> Installing it now, thanks.
>
> Given:
>
>    a set of matrixes describing the [dis]similarity
>    of individual regions on the gp120 gene of HIV-1:
>
>    C1
>
>            s1  s2  s3  s4
>
>    strain1  0  ab  ac  ad
>    strain2 ba   0  bc  bd
>    strain3 ca  cb   0  cd
>    strain4 da  db  dc  0
>
>    C2
>
>    ...
>
>    And one more providing cross-clade sample immune reponse
>    (titers produced by introducing HIV-1 clones from one
>    sample into blood from the other samples. This has a non-
>    zero diagonal.
>
> Q: Where in the bioconductor doc's would you start
>   looking for the proper package to try and correlate
>   the genetic similarity with the neutraliztion output?
>
>
> Normally you'd expect the digonal to have a maximum; you'd
> expect the off-diagnoal values to be similar (i.e., ab ~~ ba).
> Since this is HIV-1, they obviously aren't. What I'm trying
> to do now is see if there is anything we can figure out about
> the various regions that might account for the differences.
>
> Any advice would be greatly appreciated.
>
> thanx
>
> --
> Steven Lembark                                          85-09 90th St.
> Workhorse Computing                               Woodhaven, NY, 11421
> lembark@wrkhors.com                                    +1 888 359 3508
>



-- 
Amy Mikhail
Program Manager, ACTc Afghanistan Malaria Project
London School of Hygiene & Tropical Medicine

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