compile cygwin stand-alone executable

[KehindeOyeniran]

Hi I found this old forum post which indicates that it was possible to get a CL version of the old hyphy running under cygwin

http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1403088249/4

Unfortunately the link to the executable is now broken

My main question is this: Is there an available cygwin executable for the new fully CL version(s) of hyphy and if so where could this be found?

My second question is: would such an executable (if it "could" exist) be portable and self-contained enough to be distributed as a third-party addon to another program?
cheers
Kenny

[spond]

Dear @KehindeOyeniran,

V2.5.x does not come precompiled for Cygwin. But because it is a CL-only application that is pretty much self-contained, doesn't use any modules other than the standard library, it should be fairly straightforward to compile. I can take a crack at it next week. What version of Windows?

To answer the second question: I don't see why not. What do you have in mind?

Best,
Sergei

[KehindeOyeniran]

Thank you so much for your rapid reply Sergei! I would like to write a computer program that identifies coding regions within the genomes of uncalssified phages for which there are multiple homologous genomes available. I will first identify these based on a dataset of uncharacterized phages (mostly microviridae from icrobiome projects) by making a blast database of these and then scanning every genome against all the rest using tblastx. I will then fish out sets of apparently homologous orfs, align these and (after removing stop codons partial codons etc) I will test these for gene-wide evidence of negative selection. Among other approaches (looking for expression signatures up and downstream of the gene) I will use the p-value evidence of gene-wide negative selection as a proxy p-value for the existence of an expressed protein coding gene. I will then map all the tested orfs onto their native genomes together with relative supports for their expression.

In any case that is the rough idea - I am actually quite far along in the process and was fiddling with making a simple dN:dS type mutation counting test of my own but was struggling to make good use of phylogenetic information and it was therefore recommended that I instead use hyphy where this problem has already been solved.

Thank you again for the time you are taking on this.

[KehindeOyeniran]

Sorry - I realized I dd not say what windws version I am using. I ma currently using windows 7.